BackgroundPrimary ciliopathies represent a group of inherited disorders due to defects in the primary cilium, the ‘cell’s antenna’. The 100,000 Genomes Project was launched in 2012 by Genomics ...England (GEL), recruiting National Health Service (NHS) patients with eligible rare diseases and cancer. Sequence data were linked to Human Phenotype Ontology (HPO) terms entered by recruiting clinicians.MethodsEighty-three prescreened probands were recruited to the 100,000 Genomes Project suspected to have congenital malformations caused by ciliopathies in the following disease categories: Bardet-Biedl syndrome (n=45), Joubert syndrome (n=14) and ‘Rare Multisystem Ciliopathy Disorders’ (n=24). We implemented a bespoke variant filtering and analysis strategy to improve molecular diagnostic rates for these participants.ResultsWe determined a research molecular diagnosis for n=43/83 (51.8%) probands. This is 19.3% higher than previously reported by GEL (n=27/83 (32.5%)). A high proportion of diagnoses are due to variants in non-ciliopathy disease genes (n=19/43, 44.2%) which may reflect difficulties in clinical recognition of ciliopathies. n=11/83 probands (13.3%) had at least one causative variant outside the tiers 1 and 2 variant prioritisation categories (GEL’s automated triaging procedure), which would not be reviewed in standard 100,000 Genomes Project diagnostic strategies. These include four structural variants and three predicted to cause non-canonical splicing defects. Two unrelated participants have biallelic likely pathogenic variants in LRRC45, a putative novel ciliopathy disease gene.ConclusionThese data illustrate the power of linking large-scale genome sequence to phenotype information. They demonstrate the value of research collaborations in order to maximise interpretation of genomic data.
Wnt signaling is involved in numerous aspects of vertebrate development and homeostasis, including the formation and function of blood cells. Here, we show that canonical and noncanonical Wnt ...signaling pathways are present and functional in megakaryocytes (MKs), with several Wnt effectors displaying MK-restricted expression. Using the CHRF288-11 cell line as a model for human MKs, the canonical Wnt3a signal was found to induce a time and dose-dependent increase in β-catenin expression. β-catenin accumulation was inhibited by the canonical antagonist dickkopf-1 (DKK1) and by the noncanonical agonist Wnt5a. Whole genome expression analysis demonstrated that Wnt3a and Wnt5a regulated distinct patterns of gene expression in MKs, and revealed a further interplay between canonical and noncanonical Wnt pathways. Fetal liver cells derived from low-density-lipoprotein receptor-related protein 6-deficient mice (LRP6−/−), generated dramatically reduced numbers of MKs in culture of lower ploidy (2N and 4N) than wild-type controls, implicating LRP6-dependent Wnt signaling in MK proliferation and maturation. Finally, in wild-type mature murine fetal liver-derived MKs, Wnt3a potently induced proplatelet formation, an effect that could be completely abrogated by DKK1. These data identify novel extrinsic regulators of proplatelet formation, and reveal a profound role for Wnt signaling in platelet production.
•Wnt signaling is essential for MK proliferation and maturation in addition to profoundly stimulating proplatelet formation.•These observations suggest that mature megakaryocytes may be able to respond to known Wnt gradients in the osteoblastic and vascular niches.
We recently identified 68 genomic loci where common sequence variants are associated with platelet count and volume. Platelets are formed in the bone marrow by megakaryocytes, which are derived from ...hematopoietic stem cells by a process mainly controlled by transcription factors. The homeobox transcription factor MEIS1 is uniquely transcribed in megakaryocytes and not in the other lineage-committed blood cells. By ChIP-seq, we show that 5 of the 68 loci pinpoint a MEIS1 binding event within a group of 252 MK-overexpressed genes. In one such locus in DNM3, regulating platelet volume, the MEIS1 binding site falls within a region acting as an alternative promoter that is solely used in megakaryocytes, where allelic variation dictates different levels of a shorter transcript. The importance of dynamin activity to the latter stages of thrombopoiesis was confirmed by the observation that the inhibitor Dynasore reduced murine proplatelet for-mation in vitro.
The burden of cardiovascular disease (CVD) cannot be fully addressed by therapy targeting known pathophysiological pathways. Even with stringent control of all risk factors CVD events are only ...diminished by half. A number of additional pathways probably play a role in the development of CVD and might serve as novel therapeutic targets. Genome wide expression studies represent a powerful tool to identify such novel pathways. We compared the expression profiles in monocytes from twenty two young male patients with premature familial CAD with those from controls matched for age, sex and smoking status, without a family history of CVD. Since all patients were on statins and aspirin treatment, potentially affecting the expression of genes in monocytes, twelve controls were subsequently treated with simvastatin and aspirin for 6 and 2 weeks, respectively. By whole genome expression arrays six genes were identified to have differential expression in the monocytes of patients versus controls; ABCA1, ABCG1 and RGS1 were downregulated in patients, whereas ADRB2, FOLR3 and GSTM1 were upregulated. Differential expression of all genes, apart from GSTM1, was confirmed by qPCR. Aspirin and statins altered gene expression of ABCG1 and ADBR2. All finding were validated in a second group of twenty four patients and controls. Differential expression of ABCA1, RSG1 and ADBR2 was replicated. In conclusion, we identified these 3 genes to be expressed differently in CAD cases which might play a role in the pathogenesis of atherosclerotic vascular disease.
Turning genetic discoveries identified in genome-wide association (GWA) studies into biological mechanisms is an important challenge in human genetics. Many GWA signals map outside exons, suggesting ...that the associated variants may lie within regulatory regions. We applied the formaldehyde-assisted isolation of regulatory elements (FAIRE) method in a megakaryocytic and an erythroblastoid cell line to map active regulatory elements at known loci associated with hematological quantitative traits, coronary artery disease, and myocardial infarction. We showed that the two cell types exhibit distinct patterns of open chromatin and that cell-specific open chromatin can guide the finding of functional variants. We identified an open chromatin region at chromosome 7q22.3 in megakaryocytes but not erythroblasts, which harbors the common non-coding sequence variant rs342293 known to be associated with platelet volume and function. Resequencing of this open chromatin region in 643 individuals provided strong evidence that rs342293 is the only putative causative variant in this region. We demonstrated that the C- and G-alleles differentially bind the transcription factor EVI1 affecting PIK3CG gene expression in platelets and macrophages. A protein-protein interaction network including up- and down-regulated genes in Pik3cg knockout mice indicated that PIK3CG is associated with gene pathways with an established role in platelet membrane biogenesis and thrombus formation. Thus, rs342293 is the functional common variant at this locus; to the best of our knowledge this is the first such variant to be elucidated among the known platelet quantitative trait loci (QTLs). Our data suggested a molecular mechanism by which a non-coding GWA index SNP modulates platelet phenotype.
Objetivo: describir la seguridad de la colpotomía en mujeres llevadas a laparoscopia por masas benignas en términos de complicaciones intra y posoperatorias.Materiales y métodos: serie de casos que ...incluyó pacientes con masas anexiales o uterinas benignas, sometidas a laparoscopia operatoria con extracción de la pieza quirúrgica mediante colpotomía, previo consentimiento informado. Se excluyeron pacientes con fondo de saco posterior obliterado, vagina estrecha, ausencia de útero, endometriosis profunda, enfermedad inflamatoria pélvica, masas menores de 4 cm, muestreo consecutivo. Se estudiaron variables sociodemográficas, clínicas, cualitativas y cuantitativas mediante un análisis descriptivo. La investigación fue avalada por el comité de ética médica de la institución.Resultados: durante el periodo de estudio se realizaron 12 extracciones de masas pélvicas benignas por colpotomía posterior. La mediana de la edad fue de 34,3 años (Rango Intercuartílico - RIC: 29-39,5). El 50 % de las pacientes eran nulíparas. La mediana de tiempo quirúrgico fue de 127 minutos (RIC: 90-150). No se realizó ninguna conversión a laparotomía. No se presentaron complicaciones intra ni posoperatorias.Conclusiones: la colpotomía posterior es una alternativa por considerar en la extracción de masas pélvicas benignas cuando tengan un tamaño mayor a 5 cm.
Interstitial photodynamic therapy (PDT) has seen a rebirth, partially prompted by the development of photosensitizers with longer absorption wavelengths that enable the treatment of larger tissue ...volumes. Here, we study whether using diffusers with customizable longitudinal emission profiles, rather than conventional ones with flat emission profiles, improves our ability to conform the light dose to the prostate. We present a modified Cimmino linear feasibility algorithm to solve the treatment planning problem, which improves upon previous algorithms by (1) correctly minimizing the cost function that penalizes deviations from the prescribed light dose, and (2) regularizing the inverse problem. Based on this algorithm, treatment plans were obtained under a variety of light delivery scenarios using 5-15 standard or tailored diffusers. The sensitivity of the resulting light dose distributions to uncertainties in the optical properties, and the placement of diffusers was also studied. We find that tailored diffusers only marginally outperform conventional ones in terms of prostate coverage and rectal sparing. Furthermore, it is shown that small perturbations in optical properties can lead to large changes in the light dose distribution, but that those changes can be largely corrected with a simple light dose re-normalization. Finally, we find that prostate coverage is only minimally affected by small changes in diffuser placement. Our results suggest that prostate PDT is not likely to benefit from the use of tailored diffusers. Other locations with more complex geometries might see a better improvement.
Cell type-specific gene expression in humans involves complex interactions between regulatory factors and DNA at enhancers and promoters. Mapping studies for expression quantitative trait loci ...(eQTLs), transcription factors (TFs) and chromatin markers have become widely used tools for identifying gene regulatory elements, but prediction of target genes remains a major challenge. Here, we integrate genome-wide data on TF-binding sites, chromatin markers and functional annotations to predict genes associated with human eQTLs. Using the random forest classifier, we found that genomic proximity plus five TF and chromatin features are able to predict >90% of target genes within 1 megabase of eQTLs. Despite being regularly used to map target genes, proximity is not a good indicator of eQTL targets for genes 150 kilobases away, but insulators, TF co-occurrence, open chromatin and functional similarities between TFs and genes are better indicators. Using all six features in the classifier achieved an area under the specificity and sensitivity curve of 0.91, much better compared with at most 0.75 for using any single feature. We hope this study will not only provide validation of eQTL-mapping studies, but also provide insight into the molecular mechanisms explaining how genetic variation can influence gene expression.
Resumen En este trabajo se presenta un análisis numérico del acoplamiento entre una catarina motriz y una cadena con elementos de plástico en la transmisión de potencia. El estudio se realiza ...mediante análisis numérico con software de elementos finitos. El sistema considera los modelos reológicos para la caracterización del material plástico de la cadena. Con base al presente estudio se confirmó la utilidad del modelo de Marlow para casos de cadenas con elementos plásticos. Los resultados muestran las zonas de mayor concentración de esfuerzo debido al contacto entre elementos para la transmisión de potencia y definir la variación de la fuerza de contacto en función de la rotación de la catarina motriz.
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