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1.
Virchows Arch ; 474(6): 673-680, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30888490

RESUMO

Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity.


Assuntos
Variações do Número de Cópias de DNA/fisiologia , Dosagem de Genes/genética , Testes Genéticos , Sequenciamento de Nucleotídeos em Larga Escala , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mutação/genética , Patologia Molecular/métodos , Análise de Sequência de DNA/métodos
2.
J Pineal Res ; 66(4): e12543, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30584671

RESUMO

Aflatoxin B1 (AFB1) is a major food and feed contaminant that threaten public health. Previous studies indicate that AFB1 exposure disrupted oocyte maturation. However, an effective and feasible method is unavailable for protecting oocytes against toxicity of AFB1. In the present study, using in vitro matured porcine oocytes and parthenogenetic embryos as model, we confirmed that AFB1 exposure during in vitro oocyte maturation (IVM) significantly impaired both nuclear and cytoplasmic maturation in a dose- and time-dependent manner. The different concentrations of melatonin were also tested for their protective effects on oocytes against the AFB1-induced toxicity. Our results showed that supplementation of a relative high concentration of melatonin (10-3 mol/L) during IVM efficiently reversed the impaired development rate and blastocyst quality, to the levels comparable to those of the control group. Further analysis indicated that melatonin application efficiently alleviated reactive oxygen species accumulation and initiation of apoptosis induced by AFB1 exposure. In addition, disrupted GSH/GPX system, as well as inhibited mitochondrial DNA (mtDNA) replication and mitochondrial biogenesis in AFB1-treated oocytes, can be notably reversed by melatonin application. Furthermore, cumulus cells may be important in mediating the toxicity of AFB1 to oocytes, and the metabolism of AFB1 in cumulus cells can be depressed by melatonin. To the best of our knowledge, this is the first report to confirm that melatonin application can efficiently protect oocytes from AFB1-induced toxicity. Our study provides a promising and practical strategy for alleviating or reversing AFB1-induced female reproductive toxicity in both clinical treatment and domestic reproductive management.


Assuntos
Aflatoxina B1/farmacologia , Técnicas de Maturação in Vitro de Oócitos , Melatonina/farmacologia , Oócitos/citologia , Oócitos/efeitos dos fármacos , Animais , Apoptose/efeitos dos fármacos , Células Cultivadas , Células do Cúmulo/citologia , Células do Cúmulo/efeitos dos fármacos , Células do Cúmulo/metabolismo , Variações do Número de Cópias de DNA/genética , Variações do Número de Cópias de DNA/fisiologia , DNA Mitocondrial/efeitos dos fármacos , Feminino , Glutationa/metabolismo , Marcação In Situ das Extremidades Cortadas , Oócitos/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Suínos
3.
Eur Heart J ; 38(46): 3443-3448, 2017 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-29020391

RESUMO

Aims: Sudden cardiac death (SCD) is a major public health burden. Mitochondrial dysfunction has been implicated in a wide range of cardiovascular diseases including cardiomyopathy, heart failure, and arrhythmias, but it is unknown if it also contributes to SCD risk. We sought to examine the prospective association between mtDNA copy number (mtDNA-CN), a surrogate marker of mitochondrial function, and SCD risk. Methods and results: We measured baseline mtDNA-CN in 11 093 participants from the Atherosclerosis Risk in Communities (ARIC) study. mtDNA copy number was calculated from probe intensities of mitochondrial single nucleotide polymorphisms (SNP) on the Affymetrix Genome-Wide Human SNP Array 6.0. Sudden cardiac death was defined as a sudden pulseless condition presumed due to a ventricular tachyarrhythmia in a previously stable individual without evidence of a non-cardiac cause of cardiac arrest. Sudden cardiac death cases were reviewed and adjudicated by an expert committee. During a median follow-up of 20.4 years, we observed 361 SCD cases. After adjusting for age, race, sex, and centre, the hazard ratio for SCD comparing the 1st to the 5th quintiles of mtDNA-CN was 2.24 (95% confidence interval 1.58-3.19; P-trend <0.001). When further adjusting for traditional cardiovascular disease risk factors, prevalent coronary heart disease, heart rate, QT interval, and QRS duration, the association remained statistically significant. Spline regression models showed that the association was approximately linear over the range of mtDNA-CN values. No apparent interaction by race or by sex was detected. Conclusion: In this community-based prospective study, mtDNA-CN in peripheral blood was inversely associated with the risk of SCD.


Assuntos
Variações do Número de Cópias de DNA/fisiologia , DNA Mitocondrial/fisiologia , Morte Súbita Cardíaca/etiologia , Doença da Artéria Coronariana/etiologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Fatores de Risco
4.
Ter Arkh ; 89(7): 32-38, 2017.
Artigo em Russo | MEDLINE | ID: mdl-28766538

RESUMO

AIM: To determine the prevalence of amp1q21 and its relationship to the clinical manifestations of multiple myeloma (MM). SUBJECTS AND METHODS: In December 2009 to March 2016, a total 134 patients aged 30 to 81 years (median 57 years) underwent a pretreatment FISH-study of bone marrow (BM) with centromeric and locus-specific DNA probes to identify amp1q21, t(11;14), t(4;14), t(14;16), t(14;20), t(6;14), trisomies of chromosomes 5, 9, 15, del13q14, del17p13/TP53, and t(8q24)/cMYC. Induction therapy with bortezomib-containing cycles was performed. Autologous stem cell transplantation was carried out in 48 patients. The median follow-up of patients was 19.3 months (3.2-77.4 months). Disease progression was diagnosed in 69 (51.5%) patients; 12 patients also underwent FISH study during disease progression. RESULTS: At the onset of MM, amp1q21 was detected in 53 (39.6%) patients. The overall 5-year survival rate in patients with amp1q21 was almost 2 times lower than that in those without amp1q21 (43.5 and 79.4%, respectively; p=0.07). The overall 5-year survival rate in patients with one extra copy of 1q21 (only 3 copies) was 67.3%, that in those with 2 or more extra copies of 1q21 (only 4-7 copies) was 20.9% (p=0.0016). Nine (75%) of the 12 patients examined during disease progression were found to have amp1q21: 2 cases were detected in the period of progression to have amp1q21 in its absence at disease onset; 7 cases had amp1q21 both at MM onset and progression; however, the number of copies of 1q21 was unchanged. CONCLUSION: Аmp1q21 is one of the most common chromosomal abnormalities in patients with new-onset MM and may appear in the course of disease progression. The presence of аmp1q21 is an important prognostic factor and must have to be included in the diagnostic study both at disease onset and progression.


Assuntos
Bortezomib/uso terapêutico , Aberrações Cromossômicas , Mieloma Múltiplo , Antineoplásicos/uso terapêutico , CDC2-CDC28 Quinases/genética , Cromossomos Humanos Par 1/genética , Variações do Número de Cópias de DNA/fisiologia , Feminino , Transplante de Células-Tronco Hematopoéticas/métodos , Transplante de Células-Tronco Hematopoéticas/estatística & dados numéricos , Humanos , Masculino , Pessoa de Meia-Idade , Mieloma Múltiplo/diagnóstico , Mieloma Múltiplo/genética , Mieloma Múltiplo/mortalidade , Mieloma Múltiplo/cirurgia , Valor Preditivo dos Testes , Prognóstico , Indução de Remissão/métodos , Estatística como Assunto , Taxa de Sobrevida , Resultado do Tratamento
5.
Eur Neuropsychopharmacol ; 27(8): 751-758, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28647451

RESUMO

Mitochondrial dysfunction may result in a variety of diseases. The objectives here were to examine possible differences in mtDNA copy number between healthy controls and patients with depression, anxiety or stress- and adjustment disorders; the association between mtDNA copy number and disease severity at baseline; and the association between mtDNA copy number and response after an 8-week treatment (mindfulness, cognitive based therapy). A total of 179 patients in primary health care (age 20-64 years) with depression, anxiety and stress- and adjustment disorders, and 320 healthy controls (aged 19-70 years) were included in the study. Relative mtDNA copy number was measured using quantitative real-time PCR on peripheral blood samples. We found that the mean mtDNA copy number was significantly higher in patients compared to controls (84.9 vs 75.9, p<0.0001) at baseline. The difference in mtDNA copy number between patients and controls remained significant after controlling for age and sex (ß=8.13, p<0.0001; linear regression analysis). The mtDNA copy number was significantly associated with Patient Health Questionnaire (PHQ-9) scores (ß=0.57, p=0.02) at baseline. After treatment, the change in mtDNA copy number was significantly associated with the treatment response, i.e., change in Hospital Anxiety and Depression Scale (HADS-D) and PHQ-9 scores (ß=1.00, p=0.03 and ß=0.65, p=0.04, respectively), after controlling for baseline scores, age, sex, BMI, smoking status, alcohol drinking and medication. Our findings show that mtDNA copy number is associated with symptoms of depression, anxiety and stress- and adjustment disorders and treatment response in these disorders.


Assuntos
Transtornos de Adaptação/sangue , Ansiedade/sangue , DNA Mitocondrial/sangue , Depressão/sangue , Estresse Psicológico/sangue , Adulto , Análise de Variância , Variações do Número de Cópias de DNA/fisiologia , DNA Mitocondrial/genética , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Escalas de Graduação Psiquiátrica , Ensaios Clínicos Controlados Aleatórios como Assunto , Inquéritos e Questionários , Adulto Jovem
6.
PLoS One ; 12(6): e0180170, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28658273

RESUMO

Belted cattle have a circular belt of unpigmented hair and skin around their midsection. The belt is inherited as a monogenic autosomal dominant trait. We mapped the causative variant to a 37 kb segment on bovine chromosome 3. Whole genome sequence data of 2 belted and 130 control cattle yielded only one private genetic variant in the critical interval in the two belted animals. The belt-associated variant was a copy number variant (CNV) involving the quadruplication of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene. Increased copy numbers at this CNV were strongly associated with the belt phenotype in a cohort of 333 cases and 1322 controls. We hypothesized that the CNV causes aberrant expression of TWIST2 during neural crest development, which might negatively affect melanoblasts. Functional studies showed that ectopic expression of bovine TWIST2 in neural crest in transgenic zebrafish led to a decrease in melanocyte numbers. Our results thus implicate an unsuspected involvement of TWIST2 in regulating pigmentation and reveal a non-coding CNV underlying a captivating Mendelian character.


Assuntos
Região 5'-Flanqueadora/genética , Bovinos/genética , Variações do Número de Cópias de DNA/genética , Melanócitos/fisiologia , Proteína 2 Relacionada a Twist/genética , Região 5'-Flanqueadora/fisiologia , Animais , Animais Geneticamente Modificados/genética , Bovinos/crescimento & desenvolvimento , Variações do Número de Cópias de DNA/fisiologia , Feminino , Masculino , Fenótipo , Reação em Cadeia da Polimerase , Pigmentação da Pele/genética , Proteína 2 Relacionada a Twist/fisiologia , Peixe-Zebra/genética
7.
Leg Med (Tokyo) ; 25: 71-74, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28457514

RESUMO

Recent studies of copy number variations (CNVs) associated with physical features, such as body mass index, body height or bone length, have suggested that such CNVs could serve as markers in forensic cases involving unidentified individuals. However, the process of cataloging CNVs has been slow because of the cumbersome nature and low reliability of the procedures involved. Here we describe a simple quantitative real-time PCR (Q-PCR) method for screening of medicolegally useful CNVs, which does not require reference DNA with known copy number. The first step is to prepare a chimeric plasmid vector including one copy each of the single-copy gene-specific sequence as the internal standard, and the target CNV-specific sequence. To assess the validity of this new method, we analyzed CNVs in the LTBP1 and ETV6 gene regions, both of which are candidate CNVs associated with body height. The PCR efficiencies for the single-copy (reference) gene and the target CNV were similar, indicating that quantitation was reliable. Furthermore, simulated analysis of the LTBP1 CNV using mock samples prepared by mixing vectors in varying proportions showed that this analytical method allowed correct determination of the LTBP1 copy number. These results demonstrated that our simple method has considerable potential for screening of trait-related CNVs that would be useful for forensic casework.


Assuntos
Variações do Número de Cópias de DNA/genética , Variações do Número de Cópias de DNA/fisiologia , Medicina Legal , Programas de Rastreamento/métodos , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo
8.
Plant Sci ; 261: 69-79, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28554695

RESUMO

Glyphosate is considered the world's most important herbicide, but widespread and continual use has resulted in the evolution of resistance. Kochia scoparia (kochia) has evolved resistance via tandem gene amplification of glyphosate's target, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) and resistant populations have been reported from the Canadian Prairies and the Northern Great Plains. Here, we evaluated the fitness costs of EPSPS amplification in kochia by comparing susceptible and resistant full siblings from segregating F2 populations generated from within six populations. Kochia was expected to be highly diverse because of strong gene flow; however, six of the seven field-collected parents with higher EPSPS copy number were homozygous. Under competitive greenhouse conditions, the EPSPS type of the line's maternal parent showed persistent effects: delayed emergence, delayed flowering, and reductions in viable seed count and weight overall. High EPSPS copy number individuals had reduced seed count and weight, reduced competitive ability, and reduced final height in mixed stands, but better germination of the F3. However, all characteristics were highly variable and fitness costs were not constant across genetic backgrounds. In the absence of selection from glyphosate, kochia with increased EPSPS copy number will be at a competitive disadvantage in some genetic backgrounds.


Assuntos
Bassia scoparia/efeitos dos fármacos , Glicina/análogos & derivados , Resistência a Herbicidas , Herbicidas/farmacologia , 3-Fosfoshikimato 1-Carboxiviniltransferase/genética , 3-Fosfoshikimato 1-Carboxiviniltransferase/metabolismo , Bassia scoparia/enzimologia , Bassia scoparia/genética , Bassia scoparia/fisiologia , Variações do Número de Cópias de DNA/genética , Variações do Número de Cópias de DNA/fisiologia , Glicina/farmacologia , Resistência a Herbicidas/genética , Resistência a Herbicidas/fisiologia , Melhoramento Vegetal
9.
Autism Res ; 10(9): 1470-1480, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28448694

RESUMO

Autism spectrum disorder is a complex trait with a high degree of heritability as well as documented susceptibility from environmental factors. In this study the contributions of copy number variation, exposure to air pollutants, and the interaction between the two on autism risk, were evaluated in the population-based case-control Childhood Autism Risks from Genetics and Environment (CHARGE) Study. For the current investigation, we included only those CHARGE children (a) who met criteria for autism or typical development and (b) for whom our team had conducted both genetic evaluation of copy number burden and determination of environmental air pollution exposures based on mapping addresses from the pregnancy and early childhood. This sample consisted of 158 cases of children with autism and 147 controls with typical development. Multiple logistic regression models were fit with and without environmental variable-copy number burden interactions. We found no correlation between average air pollution exposure from conception to age 2 years and the child's CNV burden. We found a significant interaction in which a 1SD increase in duplication burden combined with a 1SD increase in ozone exposure was associated with an elevated autism risk (OR 3.4, P < 0.005) much greater than the increased risks associated with either genomic duplication (OR 1.85, 95% CI 1.25-2.73) or ozone (OR 1.20, 95% CI 0.93-1.54) alone. Similar results were obtained when CNV and ozone were dichotomized to compare those in the top quartile relative to those having a smaller CNV burden and lower exposure to ozone, and when exposures were assessed separately for pregnancy, the first year of life, and the second year of life. No interactions were observed for other air pollutants, even those that demonstrated main effects; ozone tends to be negatively correlated with the other pollutants examined. While earlier work has demonstrated interactions between the presence of a pathogenic CNV and an environmental exposure [Webb et al., 2016], these findings appear to be the first indication that global copy number variation may increase susceptibility to certain environmental factors, and underscore the need to consider both genomics and environmental exposures as well as the mechanisms by which each may amplify the risks for autism associated with the other. Autism Res 2017, 10: 1470-1480. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.


Assuntos
Poluição do Ar/estatística & dados numéricos , Transtorno do Espectro Autista/epidemiologia , Transtorno do Espectro Autista/fisiopatologia , Variações do Número de Cópias de DNA/fisiologia , Exposição Ambiental/estatística & dados numéricos , Estudos de Casos e Controles , Pré-Escolar , Feminino , Humanos , Masculino , Material Particulado , Gravidez
10.
Hum Mol Genet ; 26(10): 1927-1941, 2017 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-28334874

RESUMO

Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe-interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders. Long-range polymerase chain reaction (PCR) is a traditional approach to obtain CNV breakpoint junction, but this method is inefficient when challenged by structural complexity such as often found at the PLP1 locus in association with Pelizaeus-Merzbacher disease (PMD). Here we introduced 'capture and single-molecule real-time sequencing' (cap-SMRT-seq) and newly developed 'asymmetry linker-mediated nested PCR walking' (ALN-walking) for CNV breakpoint sequencing in 49 subjects with PMD-associated CNVs. Remarkably, 29 (94%) of the 31 CNV breakpoint junctions unobtainable by conventional long-range PCR were resolved by cap-SMRT-seq and ALN-walking. Notably, unexpected CNV complexities, including inter-chromosomal rearrangements that cannot be resolved by aCGH, were revealed by efficient breakpoint sequencing. These sequence-based structures of PMD-associated CNVs further support the role of DNA replicative mechanisms in CNV mutagenesis, and facilitate genotype-phenotype correlation studies. Intriguingly, the lengths of gained segments by CNVs are strongly correlated with clinical severity in PMD, potentially reflecting the functional contribution of other dosage-sensitive genes besides PLP1. Our study provides new efficient experimental approaches (especially ALN-walking) for CNV breakpoint sequencing and highlights their importance in uncovering CNV mutagenesis and pathogenesis in genomic disorders.


Assuntos
Hibridização Genômica Comparativa/métodos , Variações do Número de Cópias de DNA/genética , Variações do Número de Cópias de DNA/fisiologia , Doença de Pelizaeus-Merzbacher/genética , Sequência de Bases , Replicação do DNA , Feminino , Dosagem de Genes/genética , Duplicação Gênica/genética , Rearranjo Gênico/genética , Estudos de Associação Genética/métodos , Genoma Humano , Genômica/métodos , Humanos , Masculino , Mutação , Doença de Pelizaeus-Merzbacher/sangue , Análise de Sequência de DNA/métodos
11.
Nat Commun ; 8: 14366, 2017 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-28176757

RESUMO

Human copy number variants (CNVs) account for genome variation an order of magnitude larger than single-nucleotide polymorphisms. Although much of this variation has no phenotypic consequences, some variants have been associated with disease, in particular neurodevelopmental disorders. Pathogenic CNVs are typically very large and contain multiple genes, and understanding the cause of the pathogenicity remains a major challenge. Here we show that pathogenic CNVs are significantly enriched for genes involved in development and genes that have greater evolutionary copy number conservation across mammals, indicative of functional constraints. Conversely, genes found in benign CNV regions have more variable copy number. These evolutionary constraints are characteristic of genes in pathogenic CNVs and can only be explained by dosage sensitivity of those genes. These results implicate dosage sensitivity of individual genes as a common cause of CNV pathogenicity. These evolutionary metrics suggest a path to identifying disease genes in pathogenic CNVs.


Assuntos
Variações do Número de Cópias de DNA/fisiologia , Dosagem de Genes/fisiologia , Genoma Humano/fisiologia , Transtornos do Neurodesenvolvimento/genética , Fenótipo , Biologia Computacional/métodos , Conjuntos de Dados como Assunto , Evolução Molecular , Genômica/métodos , Humanos
12.
J Oral Pathol Med ; 46(5): 393-397, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-27682444

RESUMO

OBJECTIVE: The aim of this study was to investigate whether a variation in the genomic copy number (CNV) of the ß-defensin cluster could be associated with the pre-disposition to chronic mucocutaneous candidiasis (CMC) in Sardinian APECED patients. SUBJECTS AND METHODS: The ß-defensin copy number variation was determined by MLPA analysis in 18 Sardinian APECED patients with CMC and in 21 Sardinian controls. Statistical analyses were performed with one-way ANOVA test. RESULTS: No statistically significant results were observed between the patients and controls groups. CONCLUSIONS: According to the results we have obtained, it appears that either ß-defensin genomic CNV is not a modifier locus for CMC susceptibility in APECED patients, or any effect is too small for it to be detected using such sample size. An extensive study on APECED patients from different geographical areas might reveal the real implication of the ß-defensin CNV in the susceptibility to Candida albicans infections.


Assuntos
Candidíase Mucocutânea Crônica/genética , Variações do Número de Cópias de DNA/genética , Predisposição Genética para Doença/genética , Poliendocrinopatias Autoimunes/genética , beta-Defensinas/genética , Adolescente , Adulto , Candida albicans , Criança , Pré-Escolar , Variações do Número de Cópias de DNA/fisiologia , Feminino , Humanos , Itália , Masculino , Pessoa de Meia-Idade , Poliendocrinopatias Autoimunes/microbiologia
13.
Behav Brain Res ; 320: 97-112, 2017 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-27916687

RESUMO

It is widely believed that diet can influence the onset and severity of cognitive aging, but the optimal combination of micronutrients and molecular and cellular mechanisms remain elusive. The purpose of this study was to compare the effects of eight distinct diets, consisting of various concentrations of selected micronutrients, on learning and memory as well as markers of neuronal plasticity, and metabolic and neuro-immune status of the aged hippocampus. Eighteen-month-old male and female C57BL/6J mice were fed the diets for 16 weeks, followed by learning and memory trials on the active avoidance task. Number of immature neurons were measured by immunohistochemical detection of doublecortin (DCX+) in the granule layer of the dentate gyrus. Amount of mitochondrial DNA (mtDNA) and gene expression of molecular markers of mitochondrial biogenesis (Ppargc1α, Sirt1, Tfam), and neuroinflammation (IL-10, Alox15, Ptgs2, IL-1ß, IL-6 and Tnf) were assessed by quantitative real time polymerase chain reaction (qRT-PCR) of hippocampal samples. Tissue levels of selected micronutrients and a number of metabolites were measured by liquid chromatography-mass spectrometry. The diet supplemented with RRR d-alpha tocopheryl acetate, citicholine, 5-methyltetrahydrofolic acid, quercetin and the n-3 fatty acid phosphatidylserine-docosahexaenoic acid, improved performance on the active avoidance learning and memory task compared to all the other less-complex diets. This diet also increased IL-10 expression and attenuated the age-related change in mtDNA content in the hippocampus without affecting metabolite levels. Results suggest cognitive benefits of wholesome diets are partially mediated through combined antioxidant and anti-inflammatory activities of optimized mixtures of micronutrients.


Assuntos
Envelhecimento , Cognição/efeitos dos fármacos , Hipocampo/efeitos dos fármacos , Hipocampo/fisiologia , Micronutrientes/farmacologia , Fatores Etários , Animais , Aprendizagem da Esquiva/efeitos dos fármacos , Peso Corporal/efeitos dos fármacos , Estudos de Coortes , Citocinas/genética , Citocinas/metabolismo , Variações do Número de Cópias de DNA/fisiologia , DNA Mitocondrial/genética , Ingestão de Alimentos/efeitos dos fármacos , Feminino , Regulação da Expressão Gênica/efeitos dos fármacos , Regulação da Expressão Gênica/fisiologia , Metabolismo dos Lipídeos/efeitos dos fármacos , Masculino , Metaboloma/fisiologia , Camundongos , Camundongos Endogâmicos C57BL , Proteínas Associadas aos Microtúbulos/metabolismo , Neuropeptídeos/metabolismo , Fatores Sexuais
14.
Am J Med Genet B Neuropsychiatr Genet ; 171(6): 790-6, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-26953189

RESUMO

The role of rare genetic variants, in particular copy number variants (CNVs), in the etiology of neurodevelopmental disorders is becoming increasingly clear. While the list of these disorder-related CNVs continues to lengthen, it has also become clear that in nearly all genetic variants the proportion of carriers who express the associated phenotype is far from 100%. To understand this variable penetrance of CNVs it is important to realize that even the largest CNVs represent only a tiny fraction of the entire genome. Therefore, part of the mechanism underlying the variable penetrance of CNVs is likely the modulatory impact of the rest of the genome. In the present study we used the 22q11DS as a model to examine whether the observed penetrance of intellectual impairment-one of the main phenotypes associated with 22q11DS-is modulated by the intellectual level of their parents, for which we used the parents' highest level of education as a proxy. Our results, based on data observed in 171 children with 22q11DS in the age range of 5-15 years, showed a significant association between estimated parental cognitive level and intelligence in offspring (full scale, verbal and performance IQ), with the largest effect size for verbal IQ. These results suggest that possible mechanisms involved in the variable penetrance observed in CNVs include the impact of genetic background and/or environmental influences. © 2016 Wiley Periodicals, Inc.


Assuntos
Anormalidades Múltiplas/genética , Variações do Número de Cópias de DNA/fisiologia , Síndrome de DiGeorge/genética , Inteligência/genética , Adolescente , Criança , Pré-Escolar , Deleção Cromossômica , Cromossomos Humanos Par 22/genética , Variações do Número de Cópias de DNA/genética , Feminino , Humanos , Masculino , Transtornos Mentais/genética , Países Baixos , Pais , Penetrância , Deleção de Sequência/genética
16.
BMC Psychiatry ; 15: 50, 2015 Mar 17.
Artigo em Inglês | MEDLINE | ID: mdl-25884388

RESUMO

BACKGROUND: Several lines of evidence indicate mitochondrial impairment in the pathophysiology of autism. As one of the most common biomarkers for mitochondrial dysfunction, mitochondrial DNA (mtDNA) copy number has also been linked to autism, but the relationship between mtDNA copy number and autism was still obscured. In this study, we performed a case-control study to investigate whether mtDNA copy number in peripheral blood cells is related to patients with autism. METHODS: Relative mtDNA copy number in peripheral blood cells was measured by using real-time polymerase chain reaction method. The participants in this study included 78 patients with childhood autism and 83 typically developing children. RESULTS: We observed children with autism had significantly elevated relative mtDNA copy number than healthy controls (Beta = -0.173, P = 0.0003). However, there were no significant correlations between mtDNA copy number and clinical features (paternal age, maternal age, age of onset, illness of duration, CARS score and ABC score) in childhood autism. CONCLUSION: We show that elevated mtDNA copy number in peripheral blood is associated with autism, indicating that there may be mitochondrial dysfunction in children with autism.


Assuntos
Transtorno Autístico/etiologia , Transtorno Autístico/metabolismo , Variações do Número de Cópias de DNA/fisiologia , DNA Mitocondrial/metabolismo , Leucócitos Mononucleares/metabolismo , Doenças Mitocondriais/complicações , Estudos de Casos e Controles , Criança , Pré-Escolar , Feminino , Humanos , Masculino , Doenças Mitocondriais/metabolismo , Reação em Cadeia da Polimerase em Tempo Real
17.
J Med Genet ; 51(11): 766-772, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25280750

RESUMO

BACKGROUND: Clinical evaluation of CNVs identified via techniques such as array comparative genome hybridisation (aCGH) involves the inspection of lists of known and unknown duplications and deletions with the goal of distinguishing pathogenic from benign CNVs. A key step in this process is the comparison of the individual's phenotypic abnormalities with those associated with Mendelian disorders of the genes affected by the CNV. However, because often there is not much known about these human genes, an additional source of data that could be used is model organism phenotype data. Currently, almost 6000 genes in mouse and zebrafish are, when knocked out, associated with a phenotype in the model organism, but no disease is known to be caused by mutations in the human ortholog. Yet, searching model organism databases and comparing model organism phenotypes with patient phenotypes for identifying novel disease genes and medical evaluation of CNVs is hindered by the difficulty in integrating phenotype information across species and the lack of appropriate software tools. METHODS: Here, we present an integrated ranking scheme based on phenotypic matching, degree of overlap with known benign or pathogenic CNVs and the haploinsufficiency score for the prioritisation of CNVs responsible for a patient's clinical findings. RESULTS: We show that this scheme leads to significant improvements compared with rankings that do not exploit phenotypic information. We provide a software tool called PhenogramViz, which supports phenotype-driven interpretation of aCGH findings based on multiple data sources, including the integrated cross-species phenotype ontology Uberpheno, in order to visualise gene-to-phenotype relations. CONCLUSIONS: Integrating and visualising cross-species phenotype information on the affected genes may help in routine diagnostics of CNVs.


Assuntos
Variações do Número de Cópias de DNA/genética , Variações do Número de Cópias de DNA/fisiologia , Doença/genética , Fenótipo , Animais , Biologia Computacional , Bases de Dados Genéticas , Humanos , Camundongos , Especificidade da Espécie , Peixe-Zebra
19.
Indian J Med Res ; 139(4): 531-43, 2014 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-24927339

RESUMO

BACKGROUND & OBJECTIVES: High-risk human papilloma virus (HR-HPV) infection and its integration in host genome is a key event in malignant transformation of cervical cells. HPV16 being a dominant HR-HPV type, we undertook this study to analyze if viral load and physical state of the virus correlated with each other in the absence of other confounding variables and examined their potential as predictors of progressive cervical lesions. METHODS: Both, viral load and integration status of HPV16 were determined by real time URR PCR and estimation of E2:E6 ratio in a total of 130 PGMY-RLB -confirmed, monotypic HPV16-infected cervical DNA samples from biopsies of cytology-confirmed low grade (LSIL, 30) and high grade (HSIL, 30), and invasive carcinoma, (squamous cell carcinoma SCC, 70) cases. RESULTS: Investigation of DNA samples revealed a gradual increase in HPV16 viral load over several magnitudes and increased frequency of integration from LSIL to HSIL and HSIL to invasive cancer in relation to the severity of lesions in monotypic HPV16-infected cervical tissues. In a substantial number of precancer (11/60) and cancer cases (29/70), HPV16 was detected in concomitant mixed form. The concomitant form of HPV16 genome carried significantly higher viral load. INTERPRETATION & CONCLUSIONS: Overall, viral load and integration increased with disease severity and could be useful biomarkers in disease progression, at least, in HPV16-infected cervical pre-cancer and cancer lesions.


Assuntos
Biomarcadores/metabolismo , Carcinoma de Células Escamosas/virologia , Variações do Número de Cópias de DNA/fisiologia , Papillomavirus Humano 16/genética , Neoplasias do Colo do Útero/virologia , Integração Viral/fisiologia , Carcinoma de Células Escamosas/fisiopatologia , Feminino , Humanos , Reação em Cadeia da Polimerase em Tempo Real , Neoplasias do Colo do Útero/fisiopatologia , Carga Viral
20.
Mol Biol (Mosk) ; 47(3): 405-12, 2013 May-Jun.
Artigo em Russo | MEDLINE | ID: mdl-23888771

RESUMO

Kunitz-type proteinase inhibitor proteins of group A (KPI-A) are involved in the protection of potato plants from pathogens and pests. Although sequences of large number of the KPI-A genes from different species of cultivated potato (Solanum tuberosum subsp. tuberosum) and a few genes from tomato (Solanum lycopersicum) are known to date, information about the allelic diversity of these genes in other species of the genus Solanum is lacking. In our work, the consensus sequences of the KPI-A genes were established in two species of subgenus Potatoe sect. Petota (Solanum tuberosum subsp. andigenum--5 genes and Solanum stoloniferum--2 genes) and in the subgenus Solanum (Solanum nigrum--5 genes) by amplification, cloning, sequencing and subsequent analysis. The determined sequences of KPI-A genes were 97-100% identical to known sequences of the cultivated potato of sect. Petota (cultivated potato Solanum tuberosum subsp. tuberosum) and sect. Etuberosum (S. palustre). The interspecific variability of these genes did not exceed the intraspecific variability for all studied species except Solanum lycopersicum. The distribution of highly variable and conserved sequences in the mature protein-encoding regions was uniform for all investigated KPI-A genes. However, our attempts to amplify the homologous genes using the same primers and the genomes of Solanum dulcamarum, Solanum lycopersicum and Mandragora officinarum resulted in no product formation. Phylogenetic analysis of KPI-A diversity showed that the sequences of the S. lycopersicum form independent cluster, whereas KPI-A of S. nigrum and species of sect. Etuberosum and sect. Petota are closely related and do not form species-specific subclasters. Although Solanum nigrum is resistant to all known races of economically one of the most important diseases of solanaceous plants oomycete Phytophthora infestans aminoacid sequences encoding by KPI-A genes from its genome have nearly or absolutely no differences to the same from genomes of cultivated potatoes involved by P. infestans.


Assuntos
Variações do Número de Cópias de DNA/fisiologia , Genes de Plantas/fisiologia , Lycopersicon esculentum/genética , Peptídeos/genética , Proteínas de Plantas/genética , Solanum tuberosum/genética , Lycopersicon esculentum/metabolismo , Peptídeos/metabolismo , Proteínas de Plantas/metabolismo , Solanum tuberosum/metabolismo , Especificidade da Espécie
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