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1.
Pharmacogenomics J ; 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33649518

RESUMO

Sodium valproate (VPA) is a histone deacetylase (HDAC) inhibitor, widely prescribed in the treatment of bipolar disorder, and yet the precise modes of therapeutic action for this drug are not fully understood. After exposure of the rat serotonergic cell line RN46A to VPA, RNA-sequencing (RNA-Seq) analysis showed widespread changes in gene expression. Analysis by four bioinformatic pipelines revealed as many as 230 genes were significantly upregulated and 72 genes were significantly downregulated. A subset of 23 differentially expressed genes was selected for validation using the nCounter® platform, and of these we obtained robust validation for ADAM23, LSP1, MAOB, MMP13, PAK3, SERPINB2, SNAP91, WNT6, and ZCCHC12. We investigated the effect of lithium on this subset and found four genes, CDKN1C, LSP1, SERPINB2, and WNT6 co-regulated by lithium and VPA. We also explored the effects of other HDAC inhibitors and the VPA analogue valpromide on the subset of 23 selected genes. Expression of eight of these genes, CDKN1C, MAOB, MMP13, NGFR, SHANK3, VGF, WNT6 and ZCCHC12, was modified by HDAC inhibition, whereas others did not appear to respond to several HDAC inhibitors tested. These results suggest VPA may regulate genes through both HDAC-dependent and independent mechanisms. Understanding the broader gene regulatory effects of VPA in this serotonergic cell model should provide insights into how this drug works and whether other HDAC inhibitor compounds may have similar gene regulatory effects, as well as highlighting molecular processes that may underlie regulation of mood.

2.
Brain ; 2021 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-33704407

RESUMO

The strongest epidemiological clue that the environment at the population level has a significant impact on the risk of developing multiple sclerosis (MS) is the well-established, and in many instances, increasing latitudinal gradient of prevalence, incidence and mortality globally, with prevalence increasing by up to 10-fold between the equator and 60 degrees North and South. The drivers of this gradient are thought to be environmental with latitude seen as a proxy for ultraviolet radiation and thus vitamin D production, however other factors may also play a role. However several important questions remain unanswered, particularly when in the life course is the gradient established, does lifetime migration mitigate or exacerbate previously reported latitude gradients at location of diagnosis, and do factors such as sex or MS disease phenotype influence the timing or significance of the gradient? Utilising life time residence calendars collected as part of the New Zealand national MS prevalence study, we constructed lifetime latitudinal gradients for MS from birth to prevalence day 2006 taking into account migration internally and externally and then analysed by sex and MS clinical course phenotype. 2127 of 2917 people living in NZ on prevalence day 7 March 2006 with MS completed the life course questionnaire and of these 1587 were born in NZ. All cohorts and sub cohorts were representative of the overall MS population in NZ on prevalence day. We found that the prevalence gradient was present at birth and was in fact stronger than at census day, and the slope of the gradient persisted until the age of 12 before gradually declining. We found that internal and external migration into NZ had little if any effect on the gradient except to decrease the significance of the gradient somewhat. Finally, we found as we had reported previously that the lifetime prevalence gradients were largely driven by females with relapse onset MS. These findings confirm for the first time the importance of early life environmental exposures in the risk of MS indicating strongly that exposures as early as in utero and at birth drive the latitudinal gradient. Consequently, prevention studies should be focussed on high risk individuals and populations from the earliest possible time points especially, when appropriate, on females.

3.
Sci Rep ; 11(1): 7192, 2021 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-33785833

RESUMO

Genome wide association studies (GWAS) have identified more than 180 variants associated with breast cancer risk, however the underlying functional mechanisms and biological pathways which confer disease susceptibility remain largely unknown. As gene expression traits are under genetic regulation we hypothesise that differences in gene expression variability may identify causal breast cancer susceptibility genes. We performed variable expression quantitative trait loci (veQTL) analysis using tissue-specific expression data from the Genotype-Tissue Expression (GTEx) Common Fund Project. veQTL analysis identified 70 associations (p < 5 × 10-8) consisting of 60 genes and 27 breast cancer risk variants, including 55 veQTL that were observed in breast tissue only. Pathway analysis of genes associated with breast-specific veQTL revealed an enrichment of four genes (CYP11B1, CYP17A1 HSD3B2 and STAR) involved in the C21-steroidal biosynthesis pathway that converts cholesterol to breast-related hormones (e.g. oestrogen). Each of these four genes were significantly more variable in individuals homozygous for rs11075995 (A/A) breast cancer risk allele located in the FTO gene, which encodes an RNA demethylase. The A/A allele was also found associated with reduced expression of FTO, suggesting an epi-transcriptomic mechanism may underlie the dysregulation of genes involved in hormonal biosynthesis leading to an increased risk of breast cancer. These findings provide evidence that genetic variants govern high levels of expression variance in breast tissue, thus building a more comprehensive insight into the underlying biology of breast cancer risk loci.

4.
Cancers (Basel) ; 12(10)2020 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-33081408

RESUMO

Germline pathogenic variants in BRCA1 and BRCA2 increase cumulative lifetime risk up to 75% for breast cancer and 76% for ovarian cancer. Genetic testing for BRCA1 and BRCA2 pathogenic variants has become an important part of clinical practice for cancer risk assessment and for reducing individual risk of developing cancer. Genetic testing can produce three outcomes: positive (a pathogenic variant), uninformative (no pathogenic variant) and uncertain significance (a variant of unknown clinical significance). More than one third of BRCA1 and BRCA2 variants identified have been classified as variants of uncertain significance, presenting a challenge for clinicians. To address this important clinical challenge, a number of studies have been undertaken to establish a gene expression phenotype for pathogenic BRCA1 and BRCA2 variant carriers in several diseased and normal tissues. However, the consistency of gene expression phenotypes described in studies has been poor. To determine if gene expression analysis has been a successful approach for variant classification, we describe the design and comparability of 23 published gene expression studies that have profiled cells from BRCA1 and BRCA2 pathogenic variant carriers. We show the impact of advancements in expression-based technologies, the importance of developing larger study cohorts and the necessity to better understand variables affecting gene expression profiles across different tissue types.

5.
Lancet Psychiatry ; 7(12): 1032-1045, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33096046

RESUMO

BACKGROUND: Variation in liability to cannabis use disorder has a strong genetic component (estimated twin and family heritability about 50-70%) and is associated with negative outcomes, including increased risk of psychopathology. The aim of the study was to conduct a large genome-wide association study (GWAS) to identify novel genetic variants associated with cannabis use disorder. METHODS: To conduct this GWAS meta-analysis of cannabis use disorder and identify associations with genetic loci, we used samples from the Psychiatric Genomics Consortium Substance Use Disorders working group, iPSYCH, and deCODE (20 916 case samples, 363 116 control samples in total), contrasting cannabis use disorder cases with controls. To examine the genetic overlap between cannabis use disorder and 22 traits of interest (chosen because of previously published phenotypic correlations [eg, psychiatric disorders] or hypothesised associations [eg, chronotype] with cannabis use disorder), we used linkage disequilibrium score regression to calculate genetic correlations. FINDINGS: We identified two genome-wide significant loci: a novel chromosome 7 locus (FOXP2, lead single-nucleotide polymorphism [SNP] rs7783012; odds ratio [OR] 1·11, 95% CI 1·07-1·15, p=1·84 × 10-9) and the previously identified chromosome 8 locus (near CHRNA2 and EPHX2, lead SNP rs4732724; OR 0·89, 95% CI 0·86-0·93, p=6·46 × 10-9). Cannabis use disorder and cannabis use were genetically correlated (rg 0·50, p=1·50 × 10-21), but they showed significantly different genetic correlations with 12 of the 22 traits we tested, suggesting at least partially different genetic underpinnings of cannabis use and cannabis use disorder. Cannabis use disorder was positively genetically correlated with other psychopathology, including ADHD, major depression, and schizophrenia. INTERPRETATION: These findings support the theory that cannabis use disorder has shared genetic liability with other psychopathology, and there is a distinction between genetic liability to cannabis use and cannabis use disorder. FUNDING: National Institute of Mental Health; National Institute on Alcohol Abuse and Alcoholism; National Institute on Drug Abuse; Center for Genomics and Personalized Medicine and the Centre for Integrative Sequencing; The European Commission, Horizon 2020; National Institute of Child Health and Human Development; Health Research Council of New Zealand; National Institute on Aging; Wellcome Trust Case Control Consortium; UK Research and Innovation Medical Research Council (UKRI MRC); The Brain & Behavior Research Foundation; National Institute on Deafness and Other Communication Disorders; Substance Abuse and Mental Health Services Administration (SAMHSA); National Institute of Biomedical Imaging and Bioengineering; National Health and Medical Research Council (NHMRC) Australia; Tobacco-Related Disease Research Program of the University of California; Families for Borderline Personality Disorder Research (Beth and Rob Elliott) 2018 NARSAD Young Investigator Grant; The National Child Health Research Foundation (Cure Kids); The Canterbury Medical Research Foundation; The New Zealand Lottery Grants Board; The University of Otago; The Carney Centre for Pharmacogenomics; The James Hume Bequest Fund; National Institutes of Health: Genes, Environment and Health Initiative; National Institutes of Health; National Cancer Institute; The William T Grant Foundation; Australian Research Council; The Virginia Tobacco Settlement Foundation; The VISN 1 and VISN 4 Mental Illness Research, Education, and Clinical Centers of the US Department of Veterans Affairs; The 5th Framework Programme (FP-5) GenomEUtwin Project; The Lundbeck Foundation; NIH-funded Shared Instrumentation Grant S10RR025141; Clinical Translational Sciences Award grants; National Institute of Neurological Disorders and Stroke; National Heart, Lung, and Blood Institute; National Institute of General Medical Sciences.

6.
PLoS One ; 15(9): e0238498, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32881899

RESUMO

There are currently many tools available for capturing and defining the context of one's environment. Digital phenotyping, the use of technology and sensors to capture moment-to-moment behavior, has shown potential in quantifying the lived experience of mental illness and in the identification of individualized targets related to recovery. Environmental data suggests that greenspace may have a restorative capacity on mental health. In this paper, we explore the relationship of greenspace derived from geolocation with self-reported symptomatology from individuals with schizophrenia as well as healthy controls. Individuals with schizophrenia had less exposure to greenspace than controls, but their exposure demonstrated a dosage effect: high greenspace environments were associated with lower symptoms for anxiety (Cohen's d = -0.70), depression (d = -0.97), and psychosis (d = -0.94), whereas effect sizes for healthy controls were all negligible or small (d < 0.38). The notion that greenspace may have a more pronounced effect on individuals with mental illness presents both potential areas for recovery as well as implications for health care policy, especially in cities with a broad range of greenspace environments.


Assuntos
Ecossistema , Características de Residência/estatística & dados numéricos , Esquizofrenia/terapia , Adulto , Ansiedade , Cidades , Feminino , Humanos , Masculino , Saúde Mental , Parques Recreativos/tendências , Plantas , Psicologia do Esquizofrênico , Autorrelato , Instalações Esportivas e Recreacionais
7.
Nutrients ; 12(8)2020 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-32764253

RESUMO

Vitamin C (ascorbate) acts as an antioxidant and enzyme cofactor, and plays a vital role in human health. Vitamin C status can be affected by illness, with low levels being associated with disease due to accelerated turnover. However, robust data on the ascorbate status of patients with cancer are sparse. This study aimed to accurately measure ascorbate concentrations in plasma from patients with cancer, and determine associations with patient or tumor characteristics. We recruited 150 fasting patients with cancer (of 199 total recruited) from two cohorts, either prior to cancer surgery or during cancer chemo- or immunotherapy. A significant number of patients with cancer had inadequate plasma ascorbate concentrations. Low plasma status was more prevalent in patients undergoing cancer therapy. Ascorbate status was higher in women than in men, and exercising patients had higher levels than sedentary patients. Our study may prompt increased vigilance of ascorbate status in cancer patients.

8.
Transl Psychiatry ; 10(1): 114, 2020 04 22.
Artigo em Inglês | MEDLINE | ID: mdl-32321915

RESUMO

Cannabis use is of increasing public health interest globally. Here we examined the effect of heavy cannabis use, with and without tobacco, on genome-wide DNA methylation in a longitudinal birth cohort (Christchurch Health and Development Study, CHDS). A total of 48 heavy cannabis users were selected from the CHDS cohort, on the basis of their adult exposure to cannabis and tobacco, and DNA methylation assessed from whole blood samples, collected at approximately age 28. Methylation in heavy cannabis users was assessed, relative to non-users (n = 48 controls) via the Illumina Infinium® MethylationEPIC BeadChip. We found the most differentially methylated sites in cannabis with tobacco users were in the AHRR and F2RL3 genes, replicating previous studies on the effects of tobacco. Cannabis-only users had no evidence of differential methylation in these genes, or at any other loci at the epigenome-wide significance level (P < 10-7). However, there were 521 sites differentially methylated at P < 0.001 which were enriched for genes involved in neuronal signalling (glutamatergic synapse and long-term potentiation) and cardiomyopathy. Further, the most differentially methylated loci were associated with genes with reported roles in brain function (e.g. TMEM190, MUC3L, CDC20 and SP9). We conclude that the effects of cannabis use on the mature human blood methylome differ from, and are less pronounced than, the effects of tobacco use, and that larger sample sizes are required to investigate this further.

9.
Free Radic Res ; 54(4): 271-279, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32326774

RESUMO

Improved technology for the bioenergetic profiling of human blood cells enables population-based screening for alterations in mitochondrial respiration. Mitochondria are sensitive to oxidative stress, and the aim of this study was to quantify mitochondrial respiration in freshly isolated lymphocytes and monocytes challenged with a bolus of H2O2. Mitochondrial reserve capacity, calculated as the difference between basal oxygen consumption and maximal activity after uncoupling of the electron transport chain, was the most sensitive to H2O2. Treatment of lymphocytes with 20 µM H2O2 reduced the reserve capacity by approximately 50%, while monocyte reserve capacity was five times more resistant. Healthy donors of a similar age were tested to determine the variation between individuals, and within the same individuals tested on several different occasions. Lymphocytes obtained from a population of people aged 70-80 years showed a similar inhibition upon challenge with H2O2 as those aged 18-25 years, indicating no decline in resilience with age.


Assuntos
Peróxido de Hidrogênio/farmacologia , Linfócitos/metabolismo , Mitocôndrias/metabolismo , Monócitos/metabolismo , Consumo de Oxigênio/fisiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Humanos , Peróxido de Hidrogênio/química , Linfócitos/efeitos dos fármacos , Mitocôndrias/efeitos dos fármacos , Monócitos/efeitos dos fármacos , Oxirredução , Consumo de Oxigênio/efeitos dos fármacos , Adulto Jovem
10.
Free Radic Biol Med ; 152: 91-99, 2020 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-32142878

RESUMO

BACKGROUND: Cystic fibrosis (CF) lung disease is characterized by severe bacterial infections, excessive neutrophilic inflammation and oxidative stress. The neutrophil enzyme myeloperoxidase (MPO), which produces hypochlorous acid, is associated with worse disease outcomes. Therefore, pharmacological inhibition of MPO in the airways has therapeutic potential. We investigated whether treating mice with an MPO inhibitor during pulmonary infection decreases oxidative stress and improves infection outcomes in mice with CF-like lung inflammation without impacting on bacterial clearance. METHODS: Transgenic ß-epithelial sodium channel (ßENaC)-overexpressing mice (n = 10) were infected with Burkholderia multivorans and treated twice daily with the MPO inhibitor AZM198 (125 µmol/kg) or vehicle administered by oral gavage for two days. Bodyweight was recorded daily. MPO activity, markers of oxidative stress, inflammatory cytokines and leukocytes numbers were measured in bronchoalveolar lavage fluid (BALF). Bacterial burden was determined in lung tissue homogenates. RESULTS: During the course of infection, mice treated with AZM198 lost less weight than vehicle-treated mice (p < 0.01). MPO activity and glutathione sulfonamide, a hypochlorous acid-specific glutathione oxidation product, were significantly lower in BALF from AZM198-treated mice (p < 0.05). The inflammatory cytokines CXCL1 and TNF-α in BALF and bacterial burden in the lung were not significantly different between treated and control mice. CONCLUSIONS: Orally administered AZM198 inhibits MPO activity in epithelial lining fluid. Blocking hypochlorous acid production in epithelial lining fluid during pulmonary infections through inhibition of MPO improves morbidity in mice with CF-like lung inflammation without interfering with clearance of bacteria. Pharmacological inhibition of MPO is an approach to limit destructive oxidative stress in cystic fibrosis lung disease in humans.

11.
Dis Colon Rectum ; 63(7): 903-910, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32109915

RESUMO

BACKGROUND: The overall incidence of colorectal carcinoma is declining in Western populations; however, single country series demonstrate an increase in young-onset (<50 years) colorectal carcinoma. OBJECTIVE: The purpose of this study was to determine whether the pattern of increasing incidence of young-onset colorectal carcinoma is consistent across 3 Western populations. DESIGN: This is a population incidence study. SETTINGS: National cancer registries of New Zealand, Sweden, and Scotland were used. PATIENTS: The incidence of colorectal carcinoma was calculated from population data for 3 countries over 2 to 4 decades. MAIN OUTCOME MEASURES: The incidence of colorectal carcinoma was measured. Incidence rate ratios were determined and data were stratified by subsite (colon versus rectum), sex, and age (<50, 50-79, and ≥80 y). RESULTS: Overall colorectal carcinoma rates declined in New Zealand, remained stable in Scotland, and increased in Sweden. In all 3 populations, there was an increasing incidence of rectal carcinoma in those aged <50 years. Young-onset rectal carcinoma increased in New Zealand (1995-2012: incidence rate ratio = 1.18 (men) and 1.13 (women)), with declining incidence in all other age groups. Colon carcinoma did not increase in the population aged <50 years, with the exception of distal colonic carcinoma in men. Overall, rectal carcinoma incidence increased (1970-2014) in Sweden; however, increases in those <50 years of age exceeded increases in other age groups (incidence rate ratio = 1.14 (males) and 1.12 (females)). Distal colon carcinoma increases were most marked in the population aged <50 years. In Scotland (1990-2014), young-onset rectal carcinoma incidence increased (incidence rate ratio = 1.23 (males) and 1.27 (females)), with a smaller increase in colon carcinoma. LIMITATIONS: Limitations include its registry-based, population incidence research. CONCLUSIONS: This study shows an increase in young-onset rectal carcinoma in 3 national populations; this observation may provide a focus for looking at the role of environmental influences on the etiology of this increase and therefore to explore strategies for prevention. See Video Abstract at http://links.lww.com/DCR/B194. AUMENTO DE LA INCIDENCIA DE CARCINOMA COLORRECTAL DE INICIO JOVEN: UN ANÁLISIS DE POBLACIÓN DE TRES PAÍSES: La incidencia global de carcinoma colorrectal está disminuyendo en las poblaciones occidentales. Sin embargo, las series de un solo país demuestran un aumento en el carcinoma colorrectal de inicio joven (pacientes menores de 50 años).Determinar si el patrón de incidencia en aumento de carcinoma colorrectal de inicio joven es consistente en tres poblaciones occidentales.Estudio de incidencias de población en tres países.Registros nacionales de cáncer de Nueva Zelanda, Suecia y Escocia.la incidencia de carcinoma colorrectal se calculó a partir de datos de población de tres países durante dos o a cuatro décadas.Incidencia de carcinoma colorrectal. Se determinaron las tasas de incidencia y los datos se estratificaron por subsitio (colon versus recto), además de sexo y edad (<50, 50-79 y ≥ 80).las tasas generales de carcinoma colorrectal disminuyeron en Nueva Zelanda, se mantuvieron estables en Escocia y aumentaron en Suecia. En las tres poblaciones, hubo una incidencia creciente de carcinoma rectal en pacientes menores de 50 años. El carcinoma rectal de inicio juvenil aumentó en Nueva Zelanda (1995-2012): tasa de incidencia de 1,18 [varones] y 1,13 [mujeres], con una disminución de la incidencia en todos los demás grupos de edad. El carcinoma de colon no aumentó en la población de < 50 años, con la excepción del carcinoma de colon distal en hombres. En general, la incidencia de carcinoma rectal aumentó (1970-2014) en Suecia; sin embargo, los aumentos en aquellos de <50 años excedieron los aumentos en otros grupos de edad: tasa de incidencia 1.14 [hombres] y 1.12 [mujeres]. Los aumentos del carcinoma de colon distal fueron más marcados en la población de < 50 años. En Escocia (1990-2014), la incidencia de carcinoma rectal de inicio juvenil aumentó: relación de tasa de incidencia 1.23 [hombres] y 1.27 [mujeres], con un aumento menor en el carcinoma de colon.Investigación de incidencia poblacional basada en registros nacionales.Este estudio muestra un aumento en el carcinoma rectal de inicio joven en tres poblaciones nacionales. Esta observación puede indicar un enfoque para la examinación de influencias ambientales en la etiología de este aumento y, por lo tanto, explorar estrategias para la prevención. Consulte Video Resumen en http://links.lww.com/DCR/B194. (Traducción-Dr Adrián Ortega).

12.
N Z Med J ; 132(1507): 22-32, 2019 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-31830014

RESUMO

AIMS: To assess whether a single platelet-rich plasma (PRP) injection would reduce pain intensity in chronic greater trochanteric pain syndrome (GTPS). METHODS: Subjects with chronic lateral hip pain were randomised to either a PRP injection (intervention group) or a saline injection (control group) and both groups were prescribed identical eccentric exercise. Brief Pain Inventory (BPI), health professional consultation rate, medication use, Likert scale of progress, Expectation of Improvement Scale were assessed monthly for six months with a final follow-up one year after the intervention. RESULTS: There were no differences in any outcomes between the two groups at any follow-up point, (all p>0.39). CONCLUSION: A single injection of PRP resulted in no significant improvement for GTPS compared with a placebo injection.


Assuntos
Bursite/terapia , Fêmur/fisiopatologia , Dor Musculoesquelética/terapia , Plasma Rico em Plaquetas , Tendinopatia/terapia , Adulto , Idoso , Bursite/fisiopatologia , Feminino , Humanos , Injeções , Masculino , Pessoa de Meia-Idade , Dor Musculoesquelética/fisiopatologia , Nova Zelândia , Medição da Dor , Recuperação de Função Fisiológica , Síndrome , Tendinopatia/fisiopatologia , Resultado do Tratamento
13.
BMC Cancer ; 19(1): 1155, 2019 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-31775679

RESUMO

BACKGROUND: Post-surgical staging is the mainstay of prognostic stratification for colorectal cancer (CRC). Here, we compare TNM staging to consensus molecular subtyping (CMS) and assess the value of subtyping in addition to stratification by TNM. METHODS: Three hundred and eight treatment-naïve colorectal tumours were accessed from our institutional tissue bank. CMS typing was carried out using tumour gene-expression data. Post-surgical TNM-staging and CMS were analysed with respect to clinicopathologic variables and patient outcome. RESULTS: CMS alone was not associated with survival, while TNM stage significantly explained mortality. Addition of CMS to TNM-stratified tumours showed a prognostic effect in stage 2 tumours; CMS3 tumours had a significantly lower overall survival (P = 0.006). Stage 2 patients with a good prognosis showed immune activation and up-regulation of tumour suppressor genes. CONCLUSIONS: Although stratification using CMS does not outperform TNM staging as a prognostic indicator, gene-expression based subtyping shows promise for improved prognostication in stage 2 CRC.


Assuntos
Biomarcadores Tumorais , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/etiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/genética , Neoplasias Colorretais/mortalidade , Neoplasias Colorretais/cirurgia , Biologia Computacional/métodos , Feminino , Perfilação da Expressão Gênica/métodos , Humanos , Estimativa de Kaplan-Meier , Masculino , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Cuidados Pós-Operatórios , Prognóstico , Modelos de Riscos Proporcionais , Recidiva , Transcriptoma
14.
Pharmacogenet Genomics ; 29(9): 207-215, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31568131

RESUMO

OBJECTIVES: The MinION nanopore sequencing device opens the opportunity to cost-effective and point-of-care DNA sequencing. As a proof of principle, we developed a multiplex assay targeting pharmacogenetic variants related to clopidogrel and warfarin, the two commonly used drugs that show response variability due to genetic polymorphisms. METHODS: Six reference and 78 clinical DNA samples were amplified by PCR to generate 15 amplicons targeting 27 key variants. These products were then barcoded to enable sample multiplexing in one sequencing run. Four variant calling tools (marginCaller, VarScan 2, nanopolish, Clairvoyante) were used to compare genotyping accuracy. RESULTS: In our cohort, 81 out of 84 samples were successfully sequenced and genotyped. Using nanopolish as the variant calling tool achieved accuracy >95% for all except two variants. A known single base deletion (CYP2C9*6) was successfully detected. CONCLUSION: While minor misgenotyping issues exist, this work demonstrates that drug-specific or broad pharmacogenetic screening assays using small PCR amplicons are possible on the MinION sequencing device.


Assuntos
Sequenciamento por Nanoporos/instrumentação , Farmacogenética , Técnicas de Genotipagem , Humanos , Polimorfismo de Nucleotídeo Único/genética
15.
Pharmacogenomics ; 20(14): 1033-1047, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31559921

RESUMO

Aim: Long read sequencing offers the promise of overcoming some of the challenges in accurate genotyping of complex genes, along with the advantage of straightforward variant phasing. We have established methods for sequencing and haplotyping of the whole CYP2D6 gene using nanopore sequencing. Materials and methods: 32 samples covering various haplotypes including gene duplication were sequenced on the GridION platform. Results: Haplotypes of 52 alleles matched accurately to known star (*) allele subvariants, with the remaining 12 being assigned as new alleles, or new subvariants of known alleles. Duplicated alleles could be detected by analyzing the allelic balance. Conclusion: Nanopore sequencing of CYP2D6 offers a high throughput method for accurate haplotyping, detection of new variants and determination of duplicated alleles.


Assuntos
Citocromo P-450 CYP2D6/genética , Haplótipos/genética , Sequenciamento por Nanoporos/métodos , Alelos , Citocromo P-450 CYP2D6/isolamento & purificação , Variações do Número de Cópias de DNA/genética , Duplicação Gênica/genética , Variação Genética/genética , Genótipo , Humanos , Análise de Sequência de DNA
16.
Sci Rep ; 9(1): 12108, 2019 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-31431677

RESUMO

Natriuretic Peptides (NP) are important in maintaining normal cardiac and metabolic status and have been used to predict cardiovascular events. Whether plasma concentrations of NP products within the normal range reflect cardio-metabolic health is unknown. Plasma NTproANP, NTproBNP and NTproCNP and their bioactive counterparts were measured in a random sample of 348 community dwellers aged 49-51 yr without heart disease and associations sought with established vascular risk factors, echocardiographic indices and a genetic variant previously linked with BNP. Stratified by sex, each of ten vascular risk factors were positively associated with NTproCNP whereas associations with NTproBNP and NTproANP were all negative. In both sexes, higher plasma NTproCNP was associated with higher arterial elastance, lower LV stroke volume and lower LV end diastolic volume. Exactly opposite associations were found with plasma NTproBNP or NTproANP. Sex specific differences were identified: positive association of NTproBNP with LV end systolic volume and the negative association with LV elastance were found only in males. The genetic variant rs198358 was independently associated with NTproBNP but not with NTproANP. In conclusion, higher NTproCNP is likely to be an adaptive response to impaired LV relaxation whereas genetic factors likely contribute to higher NTproBNP and improved cardio-metabolic health at midlife.


Assuntos
Fator Natriurético Atrial/sangue , Cardiopatias/sangue , Peptídeo Natriurético Encefálico/sangue , Peptídeo Natriurético Tipo C/sangue , Fragmentos de Peptídeos/sangue , Sistema Cardiovascular/metabolismo , Sistema Cardiovascular/patologia , Feminino , Cardiopatias/epidemiologia , Cardiopatias/patologia , Humanos , Masculino , Pessoa de Meia-Idade , Peptídeos Natriuréticos/sangue , Fatores de Risco , Caracteres Sexuais
17.
J Med Genet ; 56(7): 453-460, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30890586

RESUMO

BACKGROUND: PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2-without incurring overprediction-is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. METHODS: Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212-1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant. RESULTS: We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies. CONCLUSIONS: PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.


Assuntos
Processamento Alternativo , Proteína do Grupo de Complementação N da Anemia de Fanconi/genética , Estudos de Associação Genética , Predisposição Genética para Doença , Alelos , Perfilação da Expressão Gênica , Estudos de Associação Genética/métodos , Mutação em Linhagem Germinativa , Humanos , Mutação , Neoplasias/diagnóstico , Neoplasias/genética , Degradação do RNAm Mediada por Códon sem Sentido , Sítios de Splice de RNA
18.
Int J Mol Sci ; 20(3)2019 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-30736279

RESUMO

BRCA1 and BRCA2 spliceogenic variants are often associated with an elevated risk of breast and ovarian cancers. Analyses of BRCA1 and BRCA2 splicing patterns have traditionally used technologies that sample a population of cells but do not account for the variation that may be present between individual cells. This novel proof of concept study utilises RNA in situ hybridisation to measure the absolute expression of BRCA1 and BRCA2 mRNA splicing events in single lymphoblastoid cells containing known spliceogenic variants (BRCA1c.671-2 A>G or BRCA2c.7988 A>T). We observed a large proportion of cells (>42%) in each sample that did not express mRNA for the targeted gene. Increased levels (average mRNA molecules per cell) of BRCA2 ∆17_18 were observed in the cells containing the known spliceogenic variant BRCA2c.7988 A>T, but cells containing BRCA1c.671-2 A>G were not found to express significantly increased levels of BRCA1 ∆11, as had been shown previously. Instead, we show for each variant carrier sample that a higher proportion of cells expressed the targeted splicing event compared to control cells. These results indicate that BRCA1/2 mRNA is expressed stochastically, suggesting that previously reported results using RT-PCR may have been influenced by the number of cells with BRCA1/2 mRNA expression and may not represent an elevation of constitutive mRNA expression. Detection of mRNA expression in single cells allows for a more comprehensive understanding of how spliceogenic variants influence the expression of mRNA isoforms. However, further research is required to assess the utility of this technology to measure the expression of predicted spliceogenic BRCA1 and BRCA2 variants in a diagnostic setting.


Assuntos
Processamento Alternativo , Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias da Mama/genética , RNA Mensageiro , Alelos , Linhagem Celular Tumoral , Feminino , Genótipo , Humanos , Análise de Célula Única
19.
Annu Int Conf IEEE Eng Med Biol Soc ; 2019: 1709-1712, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31946226

RESUMO

This work aims at identifying characteristic features of EEG to demarcate a microsleep from preceding responsive states. The EEG signals, after reference electrode standardization technique (REST) re-referencing, were processed through a time-varying general linear Kalman filter (TVGLKF) to derive time-varying auto-regressive (TVAR) parameters. The time-varying effective connectivity measure of orthogonal partial directed coherence (OPDC) was obtained for every instant at 256 Hz. Effective connectivity matrices formed using these OPDC measures, with the scalp electrodes as nodes were processed further using graph theory. Community-based measures were investigated and statistical significances compared. Non-parametric Wilcoxon signed rank test was used for significance analysis, with Cohen-type and Common Language effect size (CLES) as measures of effect sizes. The results showed a decrease in directional modularity from anterior to posterior, in theta, alpha, and beta bands in microsleeps. The alpha band showed the highest significance with a Cohen-type effect size of 1.25 and a median percentage difference of 23% across subjects, with a range of 13-28%. Flexibility and integration also decreased with average percentage of 25% (17-35%) and 20% (16-32%), respectively, while recruitment increased on an average of 11% (3-16%), wherever significant across all bands. These community-based measures can help characterize and explain changes in brain mechanisms, and can also serve as potential biomarkers for microsleep detection.


Assuntos
Eletroencefalografia , Encéfalo , Mapeamento Encefálico , Eletrodos , Couro Cabeludo
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