Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals

Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors

Large-scale exome-wide association analysis identifies loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases

White blood cells play diverse roles in innate and adaptive immunity. Genetic association analyses of phenotypic variation in circulating white blood cell (WBC) counts from large samples of otherwise healthy individuals can provide insights into genes and biologic pathways involved in production, differentiation, or clearance of particular WBC lineages (myeloid, lymphoid) and also potentially inform the genetic basis of autoimmune, allergic, and blood diseases. We performed an exome array-based meta-analysis of total WBC and subtype counts (neutrophils, monocytes, lymphocytes, basophils, and eosinophils) in a multi-ancestry discovery and replication sample of ∼157,622 individuals from 25 studies. We identified 16 common variants (8 of which were coding variants) associated with one or more WBC traits, the majority of which are pleiotropically associated with autoimmune diseases. Based on functional annotation, these loci included genes encoding surface markers of myeloid, lymphoid, or hematopoietic stem cell differentiation (CD69, CD33, CD87), transcription factors regulating lineage specification during hematopoiesis (ASXL1, IRF8, IKZF1, JMJD1C, ETS2-PSMG1), and molecules involved in neutrophil clearance/apoptosis (C10orf54, LTA), adhesion (TNXB), or centrosome and microtubule structure/function (KIF9, TUBD1). Together with recent reports of somatic ASXL1 mutations among individuals with idiopathic cytopenias or clonal hematopoiesis of undetermined significance, the identification of a common regulatory 3 UTR variant of ASXL1 suggests that both germline and somatic ASXL1 mutations contribute to lower blood counts in otherwise asymptomatic individuals. These association results shed light on genetic mechanisms that regulate circulating WBC counts and suggest a prominent shared genetic architecture with inflammatory and autoimmune diseases

MicroRNAs regulatory networks in cardiotoxicity

A long time and many steps are needed to bring valuable drugs to patients. Drugs not only have to be effective against the disease which they are intended for, but also safe. All drugs cause toxic effects in proportion to the dose (Paracelsus, ca. XVI cent.). Therefore, assessing carefully the optimal dose at the desired benefit/risk ratio (Stevens and Baker, 2009) and characterizing mechanisms of toxicity are essential for maintaining high safety standards. The experimental strategies used to predict drugs’ adverse events are many, and include the use of non-invasive biomarkers that can ideally be translated from test species to humans. In particular, cardiac safety requires special attentions, as it causes the cessation of drug development in over the 30% of cases due to toxic liabilities in Phase III, and over 40% post-approval (Redfern et al., 2011). In 1993 Victor Ambros, Rosalind Lee and Rhonda Feinbaum (Lee et al., 1993) described for the first time in C. elegans the role of short non-coding RNAs, called microRNAs. MicroRNAs pair with target mRNAs via sequence complementarity, and lead to mRNA degradation or translation inhibition (Filipowicz et al., 2008; Guo et al., 2010). MicroRNAs are implicated in many biological processes and in the evolution of the complexity of superior organisms, for review see (Bartel, 2004; Berezikov, 2011). Their role in cardiovascular development and diseases has been supported by an increasing number of publications, for review see (Kinet et al., 2012; Small and Olson, 2011). Recently, tissue-specific microRNAs were found in a variety of body fluids following drug-induced tissue injury (Wang et al., 2009). In particular, myocardial necrosis of different etiologies (such as acute coronary syndrome and myocardial infarction) caused an increase of heart enriched microRNAs in plasma/serum of patients, as reviewed by (McManus and Ambros, 2011). This work is aimed at increasing our knowledge about cardiac microRNAs function in different toxicological contexts and across species. Chapter 1 will give an overview of drug safety assessment focusing on the cardiovascular system, microRNAs biology and their potential as toxicity biomarkers. In Chapter 2 I will illustrate an example of drug-induced cardiac injury, and its impact on expression of microRNAs in rats’ hearts. Chronic treatment of rats with low amounts of doxorubicin (an anti-tumoral compound) caused myocardial vacuolation in ventricular tissue and a significant increase of specific microRNAs and genomic indicators of cardiomyopathy. We found that Sipa1 could be directly inhibited by miR-34c by using a luciferase assay. Notably, the phenotypic anchoring of microRNAs with histopathological read-outs in the tissue showed that over-expression of miR-216b in the heart preceded the rise of overt lesions. Chapter 3 will describe an approach to determine the distribution of mRNAs and microRNAs in different cardiac structures in rat, dog and Cynomolgus monkey. We showed that microRNAs could discriminate the different heart structures as good as mRNAs. We also assessed the expected anti-correlation between microRNAs levels and their predicted target mRNAs, and showed that mRNAs of 4 genes implicated in cardiac diseases and muscular development could be inhibited at the post-transcriptional level by 4 distinct microRNAs. We propose that our mRNAs and microRNAs data sets could be used to assess the human relevance of preclinical findings in these 3 species, and to derive potential tissue and circulating biomarkers for drug-induced cardiac injury. In conclusion, profiling microRNAs have the potential to help biomedical research in bringing drugs to patients, since they can shed light on toxicity mechanisms in the tissues (Taylor and Gant, 2008) and are a source of translatable non-invasive toxicity biomarkers in body fluids

Expression of Genes Involved in Stress, Toxicity, Inflammation, and Autoimmunity in Relation to Cadmium, Mercury, and Lead in Human Blood: A Pilot Study

There is growing evidence of immunotoxicity related to exposure to toxic trace metals, and an examination of gene expression patterns in peripheral blood samples may provide insights into the potential development of these outcomes. This pilot study aimed to correlate the blood levels of three heavy metals (mercury, cadmium, and lead) with differences in gene expression in 24 participants from the Long Island Study of Seafood Consumption. We measured the peripheral blood mRNA expression of 98 genes that are implicated in stress, toxicity, inflammation, and autoimmunity. We fit multiple linear regression models with multiple testing correction to correlate exposure biomarkers with mRNA abundance. The mean blood Hg in this cohort was 16.1 µg/L, which was nearly three times the Environmental Protection Agency (EPA) reference dose (5.8 µg/L). The levels of the other metals were consistent with those in the general population: the mean Pb was 26.8 µg/L, and the mean Cd was 0.43 µg/L. The expression of three genes was associated with mercury, four were associated with cadmium, and five were associated with lead, although none were significant after multiple testing correction. Little evidence was found to associate metal exposure with mRNA abundance for the tested genes that were associated with stress, toxicity, inflammation, or autoimmunity. Future work should provide a more complete picture of physiological reactions to heavy metal exposure

Tolerance of P. pseudoalcaligenes KF707 to metals, PCBs, and chlorobenzoates: effects on chemotaxis, biofilm and planktonic cells

La pubblicazione analizza gli effetti di composti tossici organici e inorganici sulla formazione dei biofilms e sulle cellule in sospensione del batterio P. pseudoalcaligenes KF70