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Contains fulltext : 231651.pdf (Publisher’s version ) (Open Access) In vitro neuronal models are essential for studying neurological physiology, disease mechanisms and potential treatments. Most in vitro models lack controlled vasculature, despite its necessity in brain physiology and disease. Organ-on-chip models offer microfluidic culture systems with dedicated micro-compartments for neurons and vascular cells. Such multi-cell type organs-on-chips can emulate neurovascular unit (NVU) physiology, however there is a lack of systematic data on how individual cell types are affected by culturing on microfluidic systems versus conventional culture plates. This information can provide perspective on initial findings of studies using organs-on-chip models, and further optimizes these models in terms of cellular maturity and neurovascular physiology. Here, we analysed the transcriptomic profiles of co-cultures of human induced pluripotent stem cell (hiPSC)-derived neurons and rat astrocytes, as well as one-day monocultures of human endothelial cells, cultured on microfluidic chips. For each cell type, large gene expression changes were observed when cultured on microfluidic chips compared to conventional culture plates. Endothelial cells showed decreased cell division, neurons and astrocytes exhibited increased cell adhesion, and neurons showed increased maturity when cultured on a microfluidic chip. Our results demonstrate that culturing NVU cell types on microfluidic chips changes their gene expression profiles, presumably due to distinct surface-to-volume ratios and substrate materials. These findings inform further NVU organ-on-chip model optimization and support their future application in disease studies and drug testing.

Motivation Cellular identity and behavior is controlled by complex gene regulatory networks. Transcription factors (TFs) bind to specific DNA sequences to regulate the transcription of their target genes. On the basis of these TF motifs in cis-regulatory elements we can model the influence of TFs on gene expression. In such models of TF motif activity the data is usually modeled assuming a linear relationship between the motif activity and the gene expression level. A commonly used method to model motif influence is based on Ridge Regression. One important assumption of linear regression is the independence between samples. However, if samples are generated from the same cell line, tissue, or other biological source, this assumption may be invalid. This same assumption of independence is also applied to different yet similar experimental conditions, which may also be inappropriate. In theory, the independence assumption between samples could lead to loss in signal detection. Here we investigate whether a Bayesian model that allows for correlations results in more accurate inference of motif activities. Results We extend the Ridge Regression to a Bayesian Linear Mixed Model, which allows us to model dependence between different samples. In a simulation study, we investigate the differences between the two model assumptions. We show that our Bayesian Linear Mixed Model implementation outperforms Ridge Regression in a simulation scenario where the noise, which is the signal that can not be explained by TF motifs, is uncorrelated. However, we demonstrate that there is no such gain in performance if the noise has a similar covariance structure over samples as the signal that can be explained by motifs. We give a mathematical explanation to why this is the case. Using four representative real datasets we show that at most ∼​40% of the signal is explained by motifs using the linear model. With these data there is no advantage to using the Bayesian Linear Mixed Model, due to the similarity of the covariance structure. Availability & implementation The project implementation is available at https://github.com/Sim19/SimGEXPwMotifs.

Cell-based small molecule screening is an effective strategy leading to new medicines. Scientists in the pharmaceutical industry as well as in academia have made tremendous progress in developing both large-scale and smaller-scale screening assays. However, an accessible and universal technology for measuring large numbers of molecular and cellular phenotypes in many samples in parallel is not available. Here we present the immuno-detection by sequencing (ID-seq) technology that combines antibody-based protein detection and DNA-sequencing via DNA-tagged antibodies. We use ID-seq to simultaneously measure 70 (phospho-)proteins in primary human epidermal stem cells to screen the effects of ~300 kinase inhibitor probes to characterise the role of 225 kinases. The results show an association between decreased mTOR signalling and increased differentiation and uncover 13 kinases potentially regulating epidermal renewal through distinct mechanisms. Taken together, our work establishes ID-seq as a flexible solution for large-scale high-dimensional phenotyping in fixed cell populations.

The blood group Vel was discovered 60 years ago(1), but the underlying gene is unknown. Individuals negative for the Vel antigen are rare and are required for the safe transfusion of patients with antibodies to Vel(2). To identify the responsible gene, we sequenced the exomes of five individuals negative for the Vel antigen and found that four were homozygous and one was heterozygous for a low-frequency 17-nucleotide frameshift deletion in the gene encoding the 78-amino-acid transmembrane protein SMIM1. A follow-up study showing that 59 of 64 Vel-negative individuals were homozygous for the same deletion and expression of the Vel antigen on SMIM1-transfected cells confirm SMIM1 as the gene underlying the Vel blood group. An expression quantitative trait locus (eQTL), the common SNP rs1175550 contributes to variable expression of the Vel antigen (P = 0.003) and influences the mean hemoglobin concentration of red blood cells (RBCs; P = 8.6 x 10(-15))(3). In vivo, zebrafish with smim1 knockdown showed a mild reduction in the number of RBCs, identifying SMIM1 as a new regulator of RBC formation. Our findings are of immediate relevance, as the homozygous presence of the deletion allows the unequivocal identification of Vel-negative blood donors.

ObjectivesPharmacogenetic studies of tumour necrosis factor inhibitors (TNFi) response in patients with rheumatoid arthritis (RA) have largely relied on the changes in complex disease scores, such as disease activity score 28 (DAS28), as a measure of treatment response. It is expected that genetic architecture of such complex score is heterogeneous and not very suitable for pharmacogenetic studies. We aimed to select the most optimal phenotype for TNFi response using heritability estimates.MethodsUsing two linear mixed-modelling approaches (Bayz and GCTA), we estimated heritability, together with genomic and environmental correlations for the TNFi drug-response phenotype ΔDAS28 and its separate components: Δ swollen joint count (SJC), Δ tender joint count (TJC), Δ erythrocyte sedimentation rate (ESR) and Δ visual-analogue scale of general health (VAS-GH). For this, we used genome-wide single nucleotide polymorphism (SNP) data from 878 TNFi-treated Dutch patients with RA. Furthermore, a multivariate genome-wide association study (GWAS) approach was implemented, analysing separate DAS28 components simultaneously.ResultsThe highest heritability estimates were found for ΔSJC (=0.76 and =0.87) and ΔTJC (=0.62 and =0.82); lower heritability was found for ΔDAS28 (=0.59 and =0.71) while estimates for ΔESR and ΔVASGH were near or equal to zero. The highest genomic correlations were observed for ΔSJC and ΔTJC (0.49), and the highest environmental correlation was seen between ΔTJC and ΔVASGH (0.62). The multivariate GWAS did not generate excess of low p values as compared with a univariate analysis of ΔDAS28.ConclusionsOur results indicate that multiple SNPs together explain a substantial portion of the variation in change in joint counts in TNFi-treated patients with RA. In conclusion, of the outcomes studied, the joint counts are most suitable for TNFi pharmacogenetics in RA.

Thrombocytopenia with absent radii (TAR) syndrome is a rare disorder combining specific skeletal abnormalities with a reduced platelet count. Rare proximal microdeletions of 1q21.1 are found in the majority of patients but are also found in unaffected parents. Recently it was shown that TAR syndrome is caused by the compound inheritance of a low-frequency noncoding SNP and a rare null allele in RBM8A, a gene encoding the exon-junction complex subunit member Y14 located in the deleted region. This finding provides new insight into the complex inheritance pattern and new clues to the molecular mechanisms underlying TAR syndrome. We discuss TAR syndrome in the context of abnormal phenotypes associated with proximal and distal 1q21.1 microdeletion and microduplications with incomplete penetrance and variable expressivity.

Item does not contain fulltext The exon-junction complex (EJC) performs essential RNA processing tasks. Here, we describe the first human disorder, thrombocytopenia with absent radii (TAR), caused by deficiency in one of the four EJC subunits. Compound inheritance of a rare null allele and one of two low-frequency SNPs in the regulatory regions of RBM8A, encoding the Y14 subunit of EJC, causes TAR. We found that this inheritance mechanism explained 53 of 55 cases (P < 5 x 10(-228)) of the rare congenital malformation syndrome. Of the 53 cases with this inheritance pattern, 51 carried a submicroscopic deletion of 1q21.1 that has previously been associated with TAR, and two carried a truncation or frameshift null mutation in RBM8A. We show that the two regulatory SNPs result in diminished RBM8A transcription in vitro and that Y14 expression is reduced in platelets from individuals with TAR. Our data implicate Y14 insufficiency and, presumably, an EJC defect as the cause of TAR syndrome.

Item does not contain fulltext Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we identify 75 independent genetic loci associated with one or more red blood cell phenotypes at P < 10(-8), which together explain 4-9% of the phenotypic variance per trait. Using expression quantitative trait loci and bioinformatic strategies, we identify 121 candidate genes enriched in functions relevant to red blood cell biology. The candidate genes are expressed preferentially in red blood cell precursors, and 43 have haematopoietic phenotypes in Mus musculus or Drosophila melanogaster. Through open-chromatin and coding-variant analyses we identify potential causal genetic variants at 41 loci. Our findings provide extensive new insights into genetic mechanisms and biological pathways controlling red blood cell formation and function.

Gray platelet syndrome (GPS) is a predominantly recessive platelet disorder that is characterized by mild thrombocytopenia with large platelets and a paucity of α-granules; these abnormalities cause mostly moderate but in rare cases severe bleeding. We sequenced the exomes of four unrelated individuals and identified NBEAL2 as the causative gene; it has no previously known function but is a member of a gene family that is involved in granule development. Silencing of nbeal2 in zebrafish abrogated thrombocyte formation.

Background Pain is the dominant and prevailing symptom of rheumatoid arthritis (RA). Tumor necrosis factor inihibitors (TNFi) have proven very successful in pain reduction. Interestingly, improvement of pain, is notable rapidly after administration of TNFi agents, and well before anti-inflammatory effects of treatment can be observed. The vast majority of pharmacogenetic studies of response to TNFi utilized the clinical outcome measure, disease activity score 28 (DAS28). This measure is very useful for clinical practice, however it might be less heritable as compared to individual, potentially more homogeneous, disease measures. Usage of less complex phenotypes, such as pain (heritability 28-71%), might significantly aid the identification of genetic markers predicting differential response to TNFi. Objectives We aimed to identify and replicate genetic factors predicting pain reduction upon TNFi treatment in patients with RA using genome-wide association approach. Methods We included 508 TNFi treated RA patients. Association analysis of change of visual analogue scale of pain (VAS-pain) after 14 weeks of treatment was performed on imputed genome-wide genotyping data under additive genetic model with adjustment for baseline VAS-pain. We also conducted a meta-analysis including 1287 RA patients. Gene-based analysis was performed using VEGAS. Results No findings reached the threshold for genome-wide significance (P-value≤1x10 –8 ) in the discovery cohort. Meta-analysis revealed 213 SNPs suggestively associated (P –4 ) with change in VAS-pain after fourteen weeks of TNFi treatment. The most significant SNP rs2295739 (p=2.21x10 –6 ), located ∼50kb upstream from the KCNK10 gene, which belongs to a family of genes involved in sensory perception. The top hit in the gene-based analysis was RET, known to regulate ion channels and receptors participating in detection and transduction of sensory stimuli. Besides Ret-deficient mice show elevated pain responses. Conclusions We have identified several suggestive genomic regions, further studies are required to validate if these regions play a role in pain reduction upon TNFi treatment. Disclosure of Interest : None declared DOI 10.1136/annrheumdis-2014-eular.4094

Abstract 2372 Thrombocytopenia-absent radii syndrome (TAR) is a rare congenital disorder characterized by bilateral radius aplasia and thrombocytopenia due to virtual absence of bone marrow megakaryocytes (MKs). As other blood lineages are not affected, TAR is considered to be a bone marrow failure syndrome. At birth, platelet counts are often below 50/nL, but ameliorate in many patients during the first two years of life, however, without reaching the lower norm. Platelet reactivity in reponse to thrombopoietin is abrogated, mostly when patients are young while it is restored to normal in older patients. Interestingly, this patterning is not correlated with platelet counts. In 2007 we described a microdeletion on chromosome 1q21 in all patients analyzed as necessary, but not sufficient to cause TAR, as it was also present in unaffected family members. Using next generation sequencing, we recently identified the presence of one of two single nucleotide polymorphisms (SNPs) in non-coding, regulatory regions of the gene RBM8A whose compound inheritance together with the microdeletion causes TAR syndrome (Nature Genetics, 44, 435). All patients inherited one of the two SNPs from one of one parents and the microdeletion from the other. In 25% of cases the microdeletion was acquired de novo. This gene, which is located within the microdeleted region, encodes for Y14, a major subunit of the exon junction complex. In the German/Swiss/Polish cohort of 28 patients, 20 patients had the more frequent SNP in the 5'UTR, whereas 8 patients had a previously undescribed SNP in intron 1. The 5'UTR G->A introduces a novel binding site for transcriptional repressor Evi1. This factor is expressed in megakaryocytes and still present in platelets. Using electrophoretic mobility shift assays (EMSA) with lysates from platelets we found a complex exclusively present when a labeled oligonucleotide with the 5'UTR-SNP G->C was used and not with the wildtype sequence. This complex could be partially supershifted with an anti-Evi1 antibody, suggesting that an additional factor might bind to this complex. In contrast, the intronic SNP is predicted to abrogate a binding site for Mzf1. We used EMSA with oligonucleotides of both intronic SNP and wildtype sequence and indeed found a complex binding to the wildtype sequence as well as to a consensus sequence for Mzf1, but no or reduced binding to the intronic SNP. This complex could not be supershifted by adding an anti-Mzf1 antibody. However, when nuclear extracts from Meg01 cells were used, we found that one of three subcomplexes showed reduced binding in the presence of the antibody, even when the intronic SNP was used. As both SNPs showed different binding properties we carefully evaluated clinical data and found that platelet counts were more severely reduced in patients with the 5'UTR compared to patients harboring the intronic SNP. Although case numbers for the intronic SNP are low, in a direct comparison of age-matched patients, platelet counts were always higher in TAR patients with the intronic SNP. However, we did not find any obvious differences in skeletal features between the two groups. Further work is ongoing to better understand the causative role of either SNP for impaired megakaryopoiesis and thrombocytopenia in TAR syndrome. Disclosures: No relevant conflicts of interest to declare.