RESUMEN
Developmental control of gene expression critically depends on distal cis-regulatory elements including enhancers which interact with promoters to activate gene expression. To date no global experiments have been conducted that identify their cell type and cell stage-specific activity within one developmental pathway and in a chromatin context. Here, we describe a high-throughput method that identifies thousands of differentially active cis-elements able to stimulate a minimal promoter at five stages of hematopoietic progenitor development from embryonic stem (ES) cells, which can be adapted to any ES cell derived cell type. We show that blood cell-specific gene expression is controlled by the concerted action of thousands of differentiation stage-specific sets of cis-elements which respond to cytokine signals terminating at signalling responsive transcription factors. Our work provides an important resource for studies of hematopoietic specification and highlights the mechanisms of how and where extrinsic signals program a cell type-specific chromatin landscape driving hematopoietic differentiation.
Asunto(s)
Cromatina , Secuencias Reguladoras de Ácidos Nucleicos , Cromatina/genética , Diferenciación Celular/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Regiones Promotoras Genéticas/genética , Elementos de Facilitación Genéticos/genéticaRESUMEN
Emerging pathogens of honey bees represent an important threat to the development of the beekeeping sector. The implementation of biosecurity measures in beekeeping (BMBs) plays an essential role in supporting honey bee health within the beekeeping sector. A group of experts, in collaboration with the BPRACTICES (Grant Agreement No. 696231, European Research Area on Sustainable Animal Production Systems [ERA-Net SusAn]) project partners, has provided the definition of BMBs. Thus, BMBs are all those operational activities implemented to control the risk of introduction and spread of specific honey bee disease agents. In this paper, the BMBs in the European beekeeping context are identified for the most relevant honey bee diseases in Europe: varroosis, American foulbrood (AFB), European foulbrood (EFB), nosemosis and aethinosis. Moreover, BMBs were classified in âËcategories' adapted to consider productivity and the âËOne Health' approach: human health, honey bee health and protection of the environment. The 84 BMBs described by the panel of experts were ranked according to the priority score attributed. The implementation of BMBs represents an essential step forwards to increase the resilience and sustainability of European beekeeping.
L'émergence de nouveaux agents pathogènes chez les abeilles mellifères représente une menace importante pour le développement du secteur apicole. La mise en oeuvre de mesures de biosécurité en apiculture est déterminante pour préserver la santé des abeilles mellifères dans les élevages. En collaboration avec des partenaires du projet BPRACTICES (convention de subvention n° 696231, programme ERA-Net SusAn [European Research Area on Sustainable Animal Production Systems]), un groupe d'experts a élaboré un cadre définissant ces mesures de biosécurité. Sont définies comme mesures de biosécurité en apiculture toutes les activités opérationnelles mises en oeuvre pour contrôler le risque d'introduction et de propagation d'agents pathogènes affectant spécifiquement les abeilles mellifères. Les auteurs décrivent les mesures de biosécurité applicables, dans le contexte apicole européen, aux maladies les plus importantes en Europe : la varroose, la loque américaine, la loque européenne, la nosémose et l'infestation par Aethina tumida. En outre, les mesures de biosécurité en apiculture ont été regroupées en « catégories ¼ afin de prendre en compte la productivité et l'approche « Une seule santé ¼ : santé humaine, santé des abeilles mellifères et protection de l'environnement. Les 84 mesures de biosécurité en apiculture décrites par le groupe d'experts ont été classées en fonction du niveau de priorité qui leur a été attribué. La mise en oeuvre de ces mesures représente une étape cruciale pour accroître la résilience et la durabilité de l'apiculture européenne.
Los agentes patógenos emergentes que afectan a la abeja melífera suponen una importante amenaza para el desarrollo del sector apícola. La aplicación de medidas de seguridad biológica dentro de este sector cumple una función esencial para proteger la salud de las abejas. En colaboración con asociados en el proyecto BPRACTICES (acuerdo de subvención nº 696231, programa ERA-Net SusAn [Espacio Europeo de Investigación - «Sistemas sostenibles de producción animal¼]), un grupo de expertos definió las «medidas de seguridad biológica en apicultura¼ como todas aquellas acciones realizadas para controlar el riesgo de penetración y propagación de agentes patógenos de la abeja melífera. Los autores, situándose en el contexto de la apicultura europea, exponen las medidas de seguridad biológica que ayudan a controlar las principales enfermedades de la abeja melífera en Europa: varroosis, loque americana, loque europea, nosemosis y aethinosis (infestación por el escarabajo de las colmenas). Por otra parte, estas medidas fueron divididas en diferentes «categorías¼ para poder tener en cuenta las cuestiones de productividad y el enfoque de «Una sola salud¼: salud humana, salud de la abeja melífera y protección del medio ambiente. Las 84 medidas de seguridad biológica en apicultura que describió el cuadro de expertos fueron jerarquizadas en función de una puntuación atribuida por su nivel de prioridad. La aplicación de este tipo de medidas representa un crucial paso adelante para conferir más resiliencia a la apicultura europea y hacerla más sostenible.
RESUMEN
Modern European beekeeping is facing numerous challenges due to a variety of factors, mainly related to globalisation, agrochemical pollution and environmental changes. In addition to this, new pathogens threaten the health of European honey bees. In that context, correct colony management should encompass a wider vision, where productivity aspects are linked to a One Health approach in order to protect honey bees, humans and the environment. This paper describes a novel tool to be applied in beekeeping operations: good beekeeping practices (GBPs). The authors ranked a list of GBPs scored against their importance and validated by an international team, including researchers, national animal health authorities and international beekeepers' associations. These activities were carried out in the project 'BPRACTICES', approved within the transnational call of the European Research Area Network on Sustainable Animal Production (ERA-NET SusAn) in the Horizon 2020 Research and Innovation Programme of the European Union. This study, created through an international collaboration, aims to present an innovative and implementable approach, similar to applications already adopted in other livestock production systems.
L'apiculture moderne européenne est confrontée à de nombreuses difficultés dues à divers facteurs, pour la plupart liés à la mondialisation, à la pollution agrochimique et à la modification de l'environnement. À ces facteurs s'ajoute l'émergence de nouveaux agents pathogènes qui menacent la santé des abeilles mellifères d'Europe. Dans ce contexte, une gestion appropriée des colonies d'abeilles devrait reposer sur une vision plus large, dans laquelle les aspects relevant de la productivité sont examinés suivant une approche « Une seule santé ¼ afin de protéger les abeilles mellifères, les humains et l'environnement. Les auteurs décrivent un nouvel outil destiné à l'apiculture : les bonnes pratiques apicoles. Ils ont évalué et classé par ordre d'importance une liste de bonnes pratiques apicoles validées par une équipe internationale composée de chercheurs, d'autorités nationales de la santé animale et d'associations internationales d'apiculteurs. Ces activités ont été conduites dans le cadre du projet « BPRACTICES ¼, proposition retenue suite à l'appel à projets transnationaux du réseau ERANET SusAn (European Research Area Network on Sustainable Animal Production) au sein du Programme Horizon 2020 de l'Union européenne pour la recherche et l'innovation. Conçue sous forme de collaboration internationale, cette étude vise à proposer une approche innovante et pratique, similaire aux applications précédemment adoptées dans d'autres systèmes de production animale.
La apicultura europea hace frente a numerosos problemas resultantes de diversos factores, relacionados principalmente con la mundialización, la contaminación agroquímica y los cambios ambientales, a todo lo cual se suman nuevos patógenos que amenazan la salud de las abejas melíferas europeas. En este contexto, una correcta gestión de las colonias debe traer aparejada una visión más global, en la que las cuestiones de productividad se consideren en clave de «Una sola salud¼ con objeto de proteger tanto a las abejas melíferas como a las personas y el medio ambiente. En este artículo se describe una novedosa herramienta aplicable a la actividad apícola: las buenas prácticas de apicultura. Los autores jerarquizaron una serie de buenas prácticas de apicultura seleccionadas, validadas y puntuadas según su importancia por un equipo internacional que incluía a investigadores, autoridades nacionales de sanidad animal y asociaciones internacionales de apicultores. Este trabajo formaba parte del proyecto «BPRACTICES¼, aprobado con ocasión de la convocatoria internacional abierta por la Red del espacio europeo de investigación en sanidad animal sostenible (ERANET SusAn), inscrita a su vez en Horizonte 2020, el programa de investigación e innovación de la Unión Europea. El estudio aquí descrito, fruto de la colaboración internacional, tiene por objeto presentar un planteamiento novedoso y viable, parecido a las aplicaciones ya implantadas en otros sistemas de producción animal.
Asunto(s)
Apicultura/normas , Animales , Abejas , Unión Europea , GranjasRESUMEN
Oxaliplatin-based chemotherapy is used to treat patients with esophageal adenocarcinoma (EAC), but no biomarkers are currently available for patient selection. We performed a prospective, clinical trial to identify potential biomarkers associated with clinical outcomes. Tumor tissue was obtained from 38 patients with resectable EAC before and after 2 cycles of oxaliplatin-fluorouracil chemotherapy. Pre-treatment mRNA expression of 280 DNA repair (DNAR) genes was tested for association with histopathological regression at surgery, disease-free survival (DFS) and overall survival (OS). High expression of 13 DNA damage repair genes was associated with DFS less than one year (P < 0.05); expression of 11 DNAR genes were associated with worse OS (P < 0.05). From clinical associations with outcomes, two genes, ERCC1 and EME1, were identified as candidate biomarkers. In cell lines in vitro, we showed the mechanism of action related to repair of oxaliplatin-induced DNA damage by depletion and knockout of protein binding partners of the candidate biomarkers, XPF and MUS81 respectively. In clinical samples from the clinical trial, pre-treatment XPF protein levels were associated with pathological response, and MUS81 protein was associated with 1-year DFS. XPF and MUS81 merit further validation in prospective clinical trials as biomarkers that may predict clinical response of EAC to oxaliplatin-based chemotherapy.
Asunto(s)
Adenocarcinoma/genética , Proteínas de Unión al ADN/genética , Endonucleasas/genética , Neoplasias Esofágicas/genética , Adenocarcinoma/tratamiento farmacológico , Adenocarcinoma/patología , Anciano , Protocolos de Quimioterapia Combinada Antineoplásica/administración & dosificación , Biomarcadores de Tumor/genética , Daño del ADN/efectos de los fármacos , Supervivencia sin Enfermedad , Neoplasias Esofágicas/tratamiento farmacológico , Neoplasias Esofágicas/patología , Femenino , Fluorouracilo/administración & dosificación , Humanos , Masculino , Persona de Mediana Edad , Oxaliplatino/administración & dosificación , Biosíntesis de Proteínas/efectos de los fármacosRESUMEN
Genetic defects that affect intestinal epithelial barrier function can present with very early-onset inflammatory bowel disease (VEOIBD). Using whole-genome sequencing, a novel hemizygous defect in NOX1 encoding NAPDH oxidase 1 was identified in a patient with ulcerative colitis-like VEOIBD. Exome screening of 1,878 pediatric patients identified further seven male inflammatory bowel disease (IBD) patients with rare NOX1 mutations. Loss-of-function was validated in p.N122H and p.T497A, and to a lesser degree in p.Y470H, p.R287Q, p.I67M, p.Q293R as well as the previously described p.P330S, and the common NOX1 SNP p.D360N (rs34688635) variant. The missense mutation p.N122H abrogated reactive oxygen species (ROS) production in cell lines, ex vivo colonic explants, and patient-derived colonic organoid cultures. Within colonic crypts, NOX1 constitutively generates a high level of ROS in the crypt lumen. Analysis of 9,513 controls and 11,140 IBD patients of non-Jewish European ancestry did not reveal an association between p.D360N and IBD. Our data suggest that loss-of-function variants in NOX1 do not cause a Mendelian disorder of high penetrance but are a context-specific modifier. Our results implicate that variants in NOX1 change brush border ROS within colonic crypts at the interface between the epithelium and luminal microbes.
Asunto(s)
Colon/fisiología , Genes Modificadores/genética , Genotipo , Enfermedades Inflamatorias del Intestino/genética , NADPH Oxidasa 1/genética , Animales , Niño , Preescolar , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Genoma , Secuenciación de Nucleótidos de Alto Rendimiento , Interacciones Huésped-Patógeno , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Mutación Missense/genética , Polimorfismo de Nucleótido Simple , Especies Reactivas de Oxígeno/metabolismoRESUMEN
Bladder cancers are a leading cause of death from malignancy. Molecular markers might predict disease progression and behaviour more accurately than the available prognostic factors. Here we use whole-genome sequencing to identify somatic mutations and chromosomal changes in 14 bladder cancers of different grades and stages. As well as detecting the known bladder cancer driver mutations, we report the identification of recurrent protein-inactivating mutations in CDKN1A and FAT1. The former are not mutually exclusive with TP53 mutations or MDM2 amplification, showing that CDKN1A dysfunction is not simply an alternative mechanism for p53 pathway inactivation. We find strong positive associations between higher tumour stage/grade and greater clonal diversity, the number of somatic mutations and the burden of copy number changes. In principle, the identification of sub-clones with greater diversity and/or mutation burden within early-stage or low-grade tumours could identify lesions with a high risk of invasive progression.
Asunto(s)
Cadherinas/genética , Inhibidor p21 de las Quinasas Dependientes de la Ciclina/genética , Variación Genética , Genoma/genética , Neoplasias de la Vejiga Urinaria/genética , Secuencia de Bases , Humanos , Datos de Secuencia Molecular , Mutación/genética , Clasificación del Tumor , Análisis de Secuencia de ADNRESUMEN
Colorectal cancer (CRC) is a complex disease, and therefore its development is determined by the combination of both environmental factors and genetic variants. Although genome-wide association studies (GWAS) of SNP variation have conveniently identified 20 genetic variants so far, a significant proportion of the observed heritability is yet to be explained. Common copy-number variants (CNVs) are one of the most important genomic sources of variability, and hence a potential source to explain part of this missing genetic fraction. Therefore, we have performed a GWAS on CNVs to explore the relationship between common structural variation and CRC development. Phase 1 of the GWAS consisted of 881 cases and 667 controls from a Spanish cohort. Copy-number status was validated by quantitative PCR for each of those common CNVs potentially associated with CRC in phase I. Subsequently, SNPs were chosen as proxies for the validated CNVs for phase II replication (1,342 Spanish cases and 1,874 Spanish controls). Four common CNVs were found to be associated with CRC and were further replicated in Phase II. Finally, we found that SNP rs1944682, tagging a 11q11 CNV, was nominally associated with CRC susceptibility (p value = 0.039; OR = 1.122). This locus has been previously related to extreme obesity phenotypes, which could suggest a relationship between body weight and CRC susceptibility.
Asunto(s)
Cromosomas Humanos Par 11 , Neoplasias Colorrectales/genética , Dosificación de Gen , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Polimorfismo de Nucleótido SimpleRESUMEN
Next-generation sequencing (NGS) of cancer genomes promises to revolutionise oncology, with the ability to design and use targeted drugs, to predict outcome and response, and to classify tumours. It is continually becoming cheaper, faster and more reliable, with the capability to identify rare yet clinically important somatic mutations. Technical challenges include sequencing samples of low quality and/or quantity, reliable identification of structural and copy number variation, and assessment of intratumour heterogeneity. Once these problems are overcome, the use of the data to guide clinical decision making is not straightforward, and there is a risk of premature use of molecular changes to guide patient management in the absence of supporting evidence. Paradoxically, NGS may simply move the bottleneck of personalised medicine from data acquisition to the identification of reliable biomarkers. Standardised cancer NGS data collection on an international scale would be a significant step towards optimising patient care.
Asunto(s)
Neoplasias/genética , Genoma , Humanos , Técnicas de Diagnóstico Molecular , Mutación , Neoplasias/diagnóstico , Medicina de Precisión , Análisis de Secuencia de ADNRESUMEN
The development of genotyping technologies has allowed for wider screening for inherited causes of variable outcomes following drug administration. We have performed a genome-wide association study (GWAS) on 221 colorectal cancer (CRC) patients that had been treated with 5-fluorouracil (5-FU), either alone or in combination with oxaliplatin (FOLFOX). A validation set of 791 patients was also studied. Seven SNPs (rs16857540, rs2465403, rs10876844, rs10784749, rs17626122, rs7325568 and rs4243761) showed evidence of association (pooled P-values 0.020, 9.426E-03, 0.010, 0.017, 0.042, 2.302E-04, 2.803E-03) with adverse drug reactions (ADRs). This is the first study to explore the genetic basis of inter-individual variation in toxicity responses to the administration of 5-FU or FOLFOX in CRC patients on a genome-wide scale.
Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/administración & dosificación , Neoplasias Colorrectales/tratamiento farmacológico , Neoplasias Colorrectales/genética , Fluorouracilo/administración & dosificación , Adulto , Anciano , Anciano de 80 o más Años , Biomarcadores Farmacológicos , Ensayos Clínicos Fase II como Asunto , Neoplasias Colorrectales/patología , Efectos Colaterales y Reacciones Adversas Relacionados con Medicamentos/genética , Femenino , Estudio de Asociación del Genoma Completo , Técnicas de Genotipaje , Humanos , Leucovorina/administración & dosificación , Masculino , Persona de Mediana Edad , Compuestos Organoplatinos/administración & dosificación , Farmacogenética , Polimorfismo de Nucleótido Simple/genética , Resultado del TratamientoRESUMEN
Genome-wide array approaches and sequencing analyses are powerful tools for identifying genetic aberrations in cancers, including leukemias and lymphomas. However, the clinical and biological significance of such aberrations and their subclonal distribution are poorly understood. Here, we present the first genome-wide array based study of pre-treatment and relapse samples from patients with B-cell chronic lymphocytic leukemia (B-CLL) that uses the computational statistical tool OncoSNP. We show that quantification of the proportion of copy number alterations (CNAs) and copy neutral loss of heterozygosity regions (cnLOHs) in each sample is feasible. Furthermore, we (i) reveal complex changes in the subclonal architecture of paired samples at relapse compared with pre-treatment, (ii) provide evidence supporting an association between increased genomic complexity and poor clinical outcome (iii) report previously undefined, recurrent CNA/cnLOH regions that expand or newly occur at relapse and therefore might harbor candidate driver genes of relapse and/or chemotherapy resistance. Our findings are likely to impact on future therapeutic strategies aimed towards selecting effective and individually tailored targeted therapies.
Asunto(s)
Biomarcadores de Tumor/genética , Aberraciones Cromosómicas , Células Clonales/patología , Leucemia Linfocítica Crónica de Células B/genética , Recurrencia Local de Neoplasia/genética , Polimorfismo de Nucleótido Simple/genética , Adulto , Anciano , Anciano de 80 o más Años , Femenino , Dosificación de Gen , Genoma Humano , Genómica , Humanos , Leucemia Linfocítica Crónica de Células B/terapia , Pérdida de Heterocigocidad , Masculino , Persona de Mediana Edad , Recurrencia Local de Neoplasia/terapia , Análisis de Secuencia por Matrices de Oligonucleótidos , PronósticoRESUMEN
BACKGROUND: The incidence of human papillomavirus-associated vulval neoplasia is increasing worldwide; yet the associated genetic changes remain poorly understood. METHODS: We have used single-nucleotide polymorphism microarray analysis to perform the first high-resolution investigation of genome-wide allelic imbalance in vulval neoplasia. Our sample series comprised 21 high-grade vulval intraepithelial neoplasia and 6 vulval squamous cell carcinomas, with paired non-lesional samples used to adjust for normal copy number variation. RESULTS: Overall the most common recurrent aberrations were gains at 1p and 20, with the most frequent deletions observed at 2q, 3p and 10. Copy-neutral loss of heterozygosity at 6p was a recurrent event in vulval intraepithelial neoplasia. The pattern of genetic alterations differed from the characteristic changes we previously identified in cutaneous squamous cell carcinomas. Vulval neoplasia samples did not exhibit gain at 5p, a frequent recurrent aberration in a series of cervical tumours analysed elsewhere using an identical protocol. CONCLUSION: This series of 27 vulval samples comprises the largest systematic genome-wide analysis of vulval neoplasia performed to date. Despite shared papillomavirus status and regional proximity, our data suggest that the frequency of certain genetic alterations may differ in vulval and cervical tumours.
