MicroRNAs in Platelet Physiology and Function.

Platelets are anucleate blood cells that are best known for their role in hemostasis and thrombosis. Perhaps due to the necessity of maintaining a proteome over an 8- to 9-day lifespan or the need to adapt to environmental situations, platelets retain many of the RNA metabolic processes of nucleated cells such as the ability to splice, translate, and regulate RNA levels through posttranscriptional mechanisms. In fact, in the absence of transcription, the dependence on posttranscriptional mechanisms to regulate gene expression may have resulted in microRNAs (miRNAs) making up a greater proportion of the platelet transcriptome than observed in other cells. miRNAs are ∼22 nucleotide RNA molecules that regulate gene expression through messenger RNA (mRNA) degradation or inhibition of translation. miRNAs regulate differentiation of the platelet precursor, the megakaryocyte. Identification of miRNA:mRNA pairs that are associated with platelet phenotypes has led to the discovery of novel regulators of platelet function in healthy and diseased subjects. Circulating miRNAs may originate from platelets and can serve as biomarkers for platelet function. Platelet microparticles have been demonstrated to have the ability to deliver miRNAs of extracellular targets and alter gene expression in those targets. This review summarizes the current state of knowledge of miRNAs in megakaryocytes, platelets, and platelet microparticles.

Common variants in the human platelet PAR4 thrombin receptor alter platelet function and differ by race.

Human platelets express 2 thrombin receptors: protease-activated receptor (PAR)-1 and PAR4. Recently, we reported 3.7-fold increased PAR4-mediated aggregation kinetics in platelets from black subjects compared with white subjects. We now show that platelets from blacks (n = 70) express 14% more PAR4 protein than those from whites (n = 84), but this difference is not associated with platelet PAR4 function. Quantitative trait locus analysis identified 3 common single nucleotide polymorphisms in the PAR4 gene (F2RL3) associated with PAR4-induced platelet aggregation. Among these single nucleotide polymorphisms, rs773902 determines whether residue 120 in transmembrane domain 2 is an alanine (Ala) or threonine (Thr). Compared with the Ala120 variant, Thr120 was more common in black subjects than in white subjects (63% vs 19%), was associated with higher PAR4-induced human platelet aggregation and Ca2+ flux, and generated greater inositol 1,4,5-triphosphate in transfected cells. A second, less frequent F2RL3 variant, Phe296Val, was only observed in blacks and abolished the enhanced PAR4-induced platelet aggregation and 1,4,5-triphosphate generation associated with PAR4-Thr120. PAR4 genotype did not affect vorapaxar inhibition of platelet PAR1 function, but a strong pharmacogenetic effect was observed with the PAR4-specific antagonist YD-3 [1-benzyl-3(ethoxycarbonylphenyl)-indazole]. These findings may have an important pharmacogenetic effect on the development of new PAR antagonists.

Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells.

The double membrane nuclear envelope (NE), which is contiguous with the ER, contains nuclear pore complexes (NPCs) - the channels for nucleocytoplasmic transport, and the nuclear lamina (NL) - a scaffold for NE and chromatin organization. Since numerous human diseases linked to NE proteins occur in mesenchyme-derived cells, we used proteomics to characterize NE and other subcellular fractions isolated from mesenchymal stem cells and from adipocytes and myocytes. Based on spectral abundance, we calculated enrichment scores for proteins in the NE fractions. We demonstrated by quantitative immunofluorescence microscopy that five little-characterized proteins with high enrichment scores are substantially concentrated at the NE, with Itprip exposed at the outer nuclear membrane, Smpd4 enriched at the NPC, and Mfsd10, Tmx4, and Arl6ip6 likely residing in the inner nuclear membrane. These proteins provide new focal points for studying the functions of the NE. Moreover, our datasets provide a resource for evaluating additional potential NE proteins.

PML NBs (ND10) and Daxx: from nuclear structure to protein function.

Proteins that combine PML NBs (ND10) can be divided into two groups: "transient" (that accumulate at PML NBs upon over-expression, interferon-induced up-regulation, block of proteosomal degradation, environmental stress or viral infection) and "constitutive" that co-localize with PML in the majority of cultured cells. One of the few "constitutive" components of PML NBs is the death domain-associated protein Daxx. While PML NBs are the most obvious depositories of Daxx, there are multiple alternative localization of this protein in the nucleus and cytoplasm, suggesting differential functionality of Daxx at different cellular compartments and stages of the cell cycle. The purpose of this review is to analyze Daxx spatiotemporal behavior within and outside of PML NBs and to discuss functions attributed to these localizations. We suggest that Daxx can participate in numerous cellular functions as a mediator of protein interactions, thus acting as a fine tuning instrument in highly orchestrated cellular processes; we also envision PML NBs accumulation of Daxx as an "out of action" storage depot.

Off-Target V(D)J Recombination Drives Lymphomagenesis and Is Escalated by Loss of the Rag2 C Terminus.

Genome-wide analysis of thymic lymphomas from Tp53(-/-) mice with wild-type or C-terminally truncated Rag2 revealed numerous off-target, RAG-mediated DNA rearrangements. A significantly higher fraction of these errors mutated known and suspected oncogenes/tumor suppressor genes than did sporadic rearrangements (p < 0.0001). This tractable mouse model recapitulates recent findings in human pre-B ALL and allows comparison of wild-type and mutant RAG2. Recurrent, RAG-mediated deletions affected Notch1, Pten, Ikzf1, Jak1, Phlda1, Trat1, and Agpat9. Rag2 truncation substantially increased the frequency of off-target V(D)J recombination. The data suggest that interactions between Rag2 and a specific chromatin modification, H3K4me3, support V(D)J recombination fidelity. Oncogenic effects of off-target rearrangements created by this highly regulated recombinase may need to be considered in design of site-specific nucleases engineered for genome modification.

An unbiased method for detection of genome-wide off-target effects in cell lines treated with zinc finger nucleases.

We describe a method for detecting and validating genomic aberrations arising from cell lines exposed to zinc finger nucleases (ZFNs), an important reagent used for targeted genome modifications. This method makes use of cloned cell lines, an approach that adds power when testing variables that may affect gene correction efficiency and evaluating potential side effects on a genome-wide scale. After cell treatment, the genomic DNA isolation method, as described, is ideal for high-resolution array comparative genomic hybridization (aCGH) and quantitative PCR. Guidelines for aCGH analysis and calling significant copy number variations (CNVs) for validation by qPCR are also discussed. Using this method, we describe a novel ZFN-associated chromosome 4 copy number variation (CNV) attributable to a predicted ZFN off-target cleavage site found within the CNV.

RAG2's acidic hinge restricts repair-pathway choice and promotes genomic stability.

V(D)J recombination-associated DNA double-strand breaks (DSBs) are normally repaired by the high-fidelity classical nonhomologous end-joining (cNHEJ) machinery. Previous studies implicated the recombination-activating gene (RAG)/DNA postcleavage complex (PCC) in regulating pathway choice by preventing access to inappropriate repair mechanisms such as homologous recombination (HR) and alternative NHEJ (aNHEJ). Here, we report that RAG2's "acidic hinge," previously of unknown function, is critical for several key steps. Mutations that reduce the hinge's negative charge destabilize the PCC, disrupt pathway choice, permit repair of RAG-mediated DSBs by the translocation-prone aNHEJ machinery, and reduce genomic stability in developing lymphocytes. Structural predictions and experimental results support our hypothesis that reduced flexibility of the hinge underlies these outcomes. Furthermore, sequence variants present in the human population reduce the hinge's negative charge, permit aNHEJ, and diminish genomic integrity.

A streamlined method for detecting structural variants in cancer genomes by short read paired-end sequencing.

Defining the architecture of a specific cancer genome, including its structural variants, is essential for understanding tumor biology, mechanisms of oncogenesis, and for designing effective personalized therapies. Short read paired-end sequencing is currently the most sensitive method for detecting somatic mutations that arise during tumor development. However, mapping structural variants using this method leads to a large number of false positive calls, mostly due to the repetitive nature of the genome and the difficulty of assigning correct mapping positions to short reads. This study describes a method to efficiently identify large tumor-specific deletions, inversions, duplications and translocations from low coverage data using SVDetect or BreakDancer software and a set of novel filtering procedures designed to reduce false positive calls. Applying our method to a spontaneous T cell lymphoma arising in a core RAG2/p53-deficient mouse, we identified 40 validated tumor-specific structural rearrangements supported by as few as 2 independent read pairs.

Daxx is a predominately nuclear protein that does not translocate to the cytoplasm in response to cell stress.

The intracellular translocation of Daxx to the cytoplasm is a phenomenon often attributed to cells undergoing stress, opposite to predominant nuclear localization of this protein under normal homeostatic conditions. Moreover, a number of reports have suggested that export to the cytosol upon several stress conditions, including oxidative stress, glucose deprivation and beta-amyloid peptide treatment, is indispensable for the proper execution of Daxx-induced apoptosis. On the contrary, other studies have described translocation of Daxx from cytoplasm to nucleus upon stress application. Here, we examined cellular distribution of Daxx by sub-cellular fractionation and immunofluorescent localization of endogenous protein, using SH-SY5Y neuroblastoma cell line previously reported to exhibit cytoplasmic translocation of Daxx after oxidative stress and beta-amyloid exposure. In control conditions, Daxx is an exclusively nuclear protein in SH-SY5Y cells. Short treatment by either H(2)O(2) or beta-amyloid did not show any significant change in nuclear localization of Daxx. Prolonged exposure of cells to stress compounds did not alter the intracellular deposition of Daxx that remains exclusively in the nucleus. A cohort of other cell lines, including human prostate cancer cell line DU-145, previously reported to exhibit stress-induced cytosol translocation was examined for Daxx distribution and none were confirmed to show re-localization of Daxx to the cytoplasm after either short or long stress. Time-lapse visualization of Daxx-GFP upon H(2)O(2) treatment or glucose deprivation did not show cytoplasmic translocation either. Thus, while several Daxx-dependent apoptotic mechanisms have been described, the cytosolic association and function of this protein is questionable in light of these findings.

Daxx shortens mitotic arrest caused by paclitaxel.

Resistance to the anti-neoplastic drug paclitaxel is frequent in breast cancer patients. Most studies of paclitaxel resistance have focused on pathways that elicit cellular response, while little is known about players involved in the acquirement of taxane resistance. By screening a cohort of breast cancer cell lines, we observed a correlation between level of protein Daxx and response to paclitaxel. Cells lines expressing increased level of Daxx displayed a robust paclitaxel response with nearly all cells undergoing micronucleation, while cell lines with low amount of Daxx showed a decrease in micronucleation, and accumulation in mitosis. At used paclitaxel concentrations, apoptotic levels were negligible in all cell lines tested. Human cell lines expressing anti-Daxx siRNA as well as Daxx-/- mouse fibroblasts showed similar cellular response to paclitaxel. Importantly, absence or depletion of Daxx resulted in cell survival after paclitaxel treatment, as measured by colony formation assay. We conclude that Daxx may be an important predictive factor in cellular response to paclitaxel, which emphasizes a critical but unknown function of this protein in mitotic progression, which, when disabled, leads to survival advantages upon paclitaxel treatment.