Nanomedicine-based delivery strategies for nucleic acid gene inhibitors in inflammatory diseases.

Thanks to their abilities to modulate the expression of virtually any genes, RNA therapeutics have attracted considerable research efforts. Among the strategies focusing on nucleic acid gene inhibitors, antisense oligonucleotides and small interfering RNAs have reached advanced clinical trial phases with several of them having recently been marketed. These successes were obtained by overcoming stability and cellular delivery issues using either chemically modified nucleic acids or nanoparticles. As nucleic acid gene inhibitors are promising strategies to treat inflammatory diseases, this review focuses on the barriers, from manufacturing issues to cellular/subcellular delivery, that still need to be overcome to deliver the nucleic acids to sites of inflammation other than the liver. Furthermore, key examples of applications in rheumatoid arthritis, inflammatory bowel, and lung diseases are presented as case studies of systemic, oral, and lung nucleic acid delivery.

Development of multiplexing gene silencing system using conditionally induced polycistronic synthetic antisense RNAs in Escherichia coli.

Although efficient methods of gene silencing have been established in eukaryotes, many different techniques are still used in bacteria due to the lack of a standardized tool. Here, we developed a convenient and efficient method to downregulate the expression of a specific gene using ∼140 nucleotide RNA with a 24-nucleotide antisense region from an arabinose-inducible expression plasmid by taking Escherichia coli lacZ and phoA genes encoding ß-galactosidase and alkaline phosphatase, respectively, as target genes to evaluate the model. We examined the antisense RNA (asRNA) design, including targeting position, uORF stability elements at the 5'-end, and Hfq-binding module at the 3'-end, and inducer amount required to obtain effective experimental conditions for gene silencing. Furthermore, we constructed multiplexed dual-acting asRNA genes in the plasmid, which were transcribed as polycistronic RNA and were able to knockdown multiple target genes simultaneously. We observed the highest inhibition level of 98.6% when lacZ was targeted using the pMKN104 asRNA expression plasmid, containing a five times stronger PBAD -10 promoter sequence with no requirement of the Hfq protein for repression. These features allow the system to be utilized as an asRNA expression platform in many bacteria, besides E. coli, for gene regulation.

Novel Psychoactive Phenethylamines: Impact on Genetic Material.

Psychedelic and stimulating phenethylamines belong to the family of new psychoactive substances (NPS). The acute toxicity framework has begun to be investigated, while studies showing genotoxic potential are very limited or not available. Therefore, in order to fill this gap, the aim of the present work was to evaluate the genotoxicity by treating TK6 cells with 2C-H, 2C-I, 2C-B, 25B-NBOMe, and the popular 3,4-Methylenedioxymethylamphetamine (MDMA). On the basis of cytotoxicity and cytostasis results, we selected the concentrations (6.25-35 µM) to be used in genotoxicity analysis. We used the micronucleus (MN) as indicator of genetic damage and analyzed the MNi frequency fold increase by an automated flow cytometric protocol. All substances, except MDMA, resulted genotoxic; therefore, we evaluated reactive oxygen species (ROS) induction as a possible mechanism at the basis of the demonstrated genotoxicity. The obtained results showed a statistically significant increase in ROS levels for all genotoxic phenethylamines confirming this hypothesis. Our results highlight the importance of genotoxicity evaluation for a complete assessment of the risk associated also with NPS exposure. Indeed, the subjects who do not have hazardous behaviors or require hospitalization by using active but still "safe" doses could run into genotoxicity and in the well-known long-term effects associated.

Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals.

Two different cell signals often affect transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. The most commonly used mechanistic models predict additive or multiplicative combined responses, but a systematic genome-wide evaluation of these predictions is not available. Here, we analyzed the transcriptional response of human MCF-7 cells to retinoic acid and TGF-ß, applied individually and in combination. The combined transcriptional responses of induced genes exhibited a range of behaviors, but clearly favored both additive and multiplicative outcomes. We performed paired chromatin accessibility measurements and found that increases in accessibility were largely additive. There was some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.

ß-D-glucan from marine yeast Debaryomyces hansenii BCS004 enhanced intestinal health and glucan-expressed receptor genes in Pacific red snapper Lutjanus peru.

Previous studies have shown that marine yeast Debaryomyces hansenii BCS004 (also known as Dh004) has a potential biotechnological application. The aim of this study was to investigate the structural characterization, antioxidant properties and possible health inductor of dietary ß-D-glucan BCS004. In this study, a glucan BCS004 was obtained containing (1-6)-branched (1-3)-ß-D-glucan with low molecular weight and a high purity of 90 and 91.7% for one and 4 h, respectively. ß-D-glucan BCS004 showed higher antioxidant activity, including DPPH radical and superoxide anion scavenging, ß-carotene bleaching inhibition, and iron chelation activity. An in vitro study showed that ß-D-glucan BCS004 was safe for peripheral blood leukocytes inducing proliferative effects. Moreover, in an in vivo study using ß-D-glucan BCS004 no histopathological damages or intestinal inflammation were observed in fish. The gene expression analysis highlighted that dietary ß-D-glucan BCS004 could also up-regulate glucan and macrophage receptor genes in intestine, such as C-type lectin (CTL) and macrophage mannose receptors (MMR). Overall, the results demonstrated that ß-D-glucan from D. hansenii BCS004 could be an immunostimulant with antioxidant properties and beneficial effects on intestinal health in fish.

Systems biology and network pharmacology of frailty reveal novel epigenetic targets and mechanisms.

Frailty is an age-associated condition, characterized by an inappropriate response to stress that results in a higher frequency of adverse outcomes (e.g., mortality, institutionalization and disability). Some light has been shed over its genetic background, but this is still a matter of debate. In the present study, we used network biology to analyze the interactome of frailty-related genes at different levels to relate them with pathways, clinical deficits and drugs with potential therapeutic implications. Significant pathways involved in frailty: apoptosis, proteolysis, muscle proliferation, and inflammation; genes as FN1, APP, CREBBP, EGFR playing a role as hubs and bottlenecks in the interactome network and epigenetic factors as HIST1H3 cluster and miR200 family were also involved. When connecting clinical deficits and genes, we identified five clusters that give insights into the biology of frailty: cancer, glucocorticoid receptor, TNF-α, myostatin, angiotensin converter enzyme, ApoE, interleukine-12 and -18. Finally, when performing network pharmacology analysis of the target nodes, some compounds were identified as potentially therapeutic (e.g., epigallocatechin gallate and antirheumatic agents); while some other substances appeared to be toxicants that may be involved in the development of this condition.

Hydrogen sulfide regulates circadian-clock genes in C2C12 myotubes and the muscle of high-fat-diet-fed mice.

Hydrogen sulfide (H2S) is an endogenous novel gasotransmitter which is implicated in the pathophysiology of the metabolic syndrome. Core clock genes (CCG) and its controlled genes disruption is implicated in the progression of metabolic syndrome. We examined whether H2S has any effect on CCG in the skeletal muscle of mice fed a high-fat diet (HFD) and in myotubes. In the muscle of HFD-mice, the expression of H2S biosynthesis enzyme genes (CSE, CBS, and 3-Mpst) along with antioxidant genes (GCLC, GCLM, GSS, and GSR) involved in GSH biosynthesis and recycling were reduced significantly, but the oxidative stress (OS) increased. Expression of the CCG (Bmal1, Clock, RORα, Cry2, Per2) and clock-controlled genes (PPARγ, PGC-1α, RXRα) was downregulated, whereas the levels of PPARα mRNA were upregulated. Similar to that in the muscle of HFD-mice, in vitro myotubes exposed to high glucose or palmitate to mimic metabolic syndrome, showed an increased OS and decreased in CSE mRNA, H2S production and CCG mRNA levels were also downregulated. TNF and MCP-1 treatment on the myotubes was similar to that observed in HFD-muscle, with that the Rev-erbα mRNA was upregulated. Inhibition (siRNA/pharmacological inhibitors) of both CSE and GCLC (the rate-limiting enzyme in GSH biosynthesis) decreased H2S, and increased OS; Bmal1 and Clock mRNA levels were downregulated, while Rev-erbα increased significantly in these conditions. CSE KD myotubes were post-treated with an H2S donor partially restored the mRNA levels of core clock genes. These findings report that the deficiencies of H2S/GSH impair expression of CCG and treatment with H2S donor or GSH precursor exert a positive effect over CCG. Thus, suggest that H2S as a new endogenous factor for regulating circadian clock, and its donors could provide a novel chrono-pharmacological therapy to manage metabolic disorders.

Characterization of the responses of the caspase 2, 3, 6 and 8 genes to immune challenges and extracellular ATP stimulation in the Japanese flounder (Paralichthys olivaceus).

BACKGROUND: Caspases are a family of conserved intracellular cysteine-dependent aspartate-specific cysteine proteases that play important roles in regulating cell death and inflammation. Our previous study revealed the importance of the inflammatory caspase 1 gene in extracellular ATP-mediated immune signaling in Japanese flounder, Paralichthys olivaceus. To explore the potential roles of other caspases in P. olivaceus innate immunity, we extended our study by characterizing of the responses of four additional P. olivaceus caspase genes, termed JfCaspase 2, 3, 6 and 8, to inflammatory challenge and extracellular ATP stimulation. RESULTS: Sequence analysis revealed that the domain structures of all the Japanese flounder caspase proteins are evolutionarily conserved. Quantitative real-time PCR analysis showed that the JfCaspase 2, 3, 6 and 8 genes were expressed ubiquitously but at unequal levels in all examined Japanese flounder normal tissues. In addition, the basal gene expression levels of JfCaspase 2, 3, 6 and 8 were higher than those of JfCaspase 1 in both Japanese flounder head kidney macrophages (HKMs) and peripheral blood leukocytes (PBLs). Furthermore, immune challenge experiments showed that the inflammatory stimuli LPS and poly(I:C) significantly modulated the expression of the JfCaspase 2, 3, 6 and 8 genes in Japanese flounder immune cells. Finally, DNA fragmentation, associated with increased extracellular ATP-induced JfCaspase 2, 3, 6 and 8 gene expression and enzymatic activity, was inhibited by the caspase inhibitor Z-VAD-FMK in the HKMs. CONCLUSION: Our findings demonstrate broad participation of multiple caspase genes in response to inflammatory stimulation in Japanese flounder immune cells and provide new evidence for the involvement of caspase(s) in extracellular ATP-induced apoptosis in fish.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

Antimicrobial susceptibility profile and research of mec A and erm genes in coagulase-negative staphylococci isolated from platelet concentrates bags

Abstract In recent years, several studies have described the clinical impact of bacterial infection associated with transfusion of platelet concentrates (PCs). Among the blood components, PCs are responsible for the highest rates of bacterial contamination as well as septic transfusion reactions. We assessed antimicrobial susceptibility profile, resistance to methicillin (MRCoNS), and resistance to macrolides, lincosamides and streptogramins of group B (MLSB) of 16 coagulase-negative staphylococci (CoNS) isolates from an investigation in 691 PCs bags. We then compared conventional and automated phenotypic methods, disc diffusion test (DD) and VITEK(r) 2, respectively as well as phenotypic and genotypic methods (Polymerase Chain Reaction - PCR). All CoNS were susceptible to vancomycin. The disc diffusion test characterized 18.75% as MRCoNS and 37.5% with inducible resistance to MLSB (iMLSB), and with VITEK(r) 2, 6.3% and 31.25%, respectively. The mecA gene was detected in 18.75% and the erm gene in 31.25% of the isolates. In this study, we found equal percentage values between presence of the mecA gene by PCR and resistance to methicillin using cefoxitin by DD test, evidence of the erm gene by PCR, and iMLSB resistance by automation (VITEK(r) 2). Moreover, we identified three strains with beta-lactamase overproduction, and the occurrence of a bigger mistake was verified when automation was compared with DD test. And we observed that D-test was the most reliable for the detection of iMLSB resistance in Staphylococcus sp.

Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α).

Viruses that infect birds pose major threats-to the global supply of chicken, the major, universally-acceptable meat, and as zoonotic agents (e.g. avian influenza viruses H5N1 and H7N9). Controlling these viruses in birds as well as understanding their emergence into, and transmission amongst, humans will require considerable ingenuity and understanding of how different species defend themselves. The type I interferon-coordinated response constitutes the major antiviral innate defence. Although interferon was discovered in chicken cells, details of the response, particularly the identity of hundreds of stimulated genes, are far better described in mammals. Viruses induce interferon-stimulated genes but they also regulate the expression of many hundreds of cellular metabolic and structural genes to facilitate their replication. This study focusses on the potentially anti-viral genes by identifying those induced just by interferon in primary chick embryo fibroblasts. Three transcriptomic technologies were exploited: RNA-seq, a classical 3'-biased chicken microarray and a high density, "sense target", whole transcriptome chicken microarray, with each recognising 120-150 regulated genes (curated for duplication and incorrect assignment of some microarray probesets). Overall, the results are considered robust because 128 of the compiled, curated list of 193 regulated genes were detected by two, or more, of the technologies.

DGIdb 2.0: mining clinically relevant drug-gene interactions.

The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that consolidates disparate data sources describing drug-gene interactions and gene druggability. It provides an intuitive graphical user interface and a documented application programming interface (API) for querying these data. DGIdb was assembled through an extensive manual curation effort, reflecting the combined information of twenty-seven sources. For DGIdb 2.0, substantial updates have been made to increase content and improve its usefulness as a resource for mining clinically actionable drug targets. Specifically, nine new sources of drug-gene interactions have been added, including seven resources specifically focused on interactions linked to clinical trials. These additions have more than doubled the overall count of drug-gene interactions. The total number of druggable gene claims has also increased by 30%. Importantly, a majority of the unrestricted, publicly-accessible sources used in DGIdb are now automatically updated on a weekly basis, providing the most current information for these sources. Finally, a new web view and API have been developed to allow searching for interactions by drug identifiers to complement existing gene-based search functionality. With these updates, DGIdb represents a comprehensive and user friendly tool for mining the druggable genome for precision medicine hypothesis generation.

ZINC 15--Ligand Discovery for Everyone.

Many questions about the biological activity and availability of small molecules remain inaccessible to investigators who could most benefit from their answers. To narrow the gap between chemoinformatics and biology, we have developed a suite of ligand annotation, purchasability, target, and biology association tools, incorporated into ZINC and meant for investigators who are not computer specialists. The new version contains over 120 million purchasable "drug-like" compounds--effectively all organic molecules that are for sale--a quarter of which are available for immediate delivery. ZINC connects purchasable compounds to high-value ones such as metabolites, drugs, natural products, and annotated compounds from the literature. Compounds may be accessed by the genes for which they are annotated as well as the major and minor target classes to which those genes belong. It offers new analysis tools that are easy for nonspecialists yet with few limitations for experts. ZINC retains its original 3D roots--all molecules are available in biologically relevant, ready-to-dock formats. ZINC is freely available at http://zinc15.docking.org.

Next-Generation Transcriptome Profiling of the Salmon Louse Caligus rogercresseyi Exposed to Deltamethrin (AlphaMax™): Discovery of Relevant Genes and Sex-Related Differences.

Sea lice are one of the main parasites affecting the salmon aquaculture industry, causing significant economic losses worldwide. Increased resistance to traditional chemical treatments has created the need to find alternative control methods. Therefore, the objective of this study was to identify the transcriptome response of the salmon louse Caligus rogercresseyi to the delousing drug deltamethrin (AlphaMax™). Through bioassays with different concentrations of deltamethrin, adult salmon lice transcriptomes were sequenced from cDNA libraries in the MiSeq Illumina platform. A total of 78 million reads for females and males were assembled in 30,212 and 38,536 contigs, respectively. De novo assembly yielded 86,878 high-quality contigs and, based on published data, it was possible to annotate and identify relevant genes involved in several biological processes. RNA-seq analysis in conjunction with heatmap hierarchical clustering evidenced that pyrethroids modify the ectoparasitic transcriptome in adults, affecting molecular processes associated with the nervous system, cuticle formation, oxidative stress, reproduction, and metabolism, among others. Furthermore, sex-related transcriptome differences were evidenced. Specifically, 534 and 1033 exclusive transcripts were identified for males and females, respectively, and 154 were shared between sexes. For males, estradiol 17-beta-dehydrogenase, sphingolipid delta4-desaturase DES1, ketosamine-3-kinase, and arylsulfatase A, among others, were discovered, while for females, vitellogenin 1, glycoprotein G, transaldolase, and nitric oxide synthase were among those identified. The shared transcripts included annotations for tropomyosin, γ-crystallin A, glutamate receptor-metabotropic, glutathione S-transferase, and carboxipeptidase B. The present study reveals that deltamethrin generates a complex transcriptome response in C. rogercresseyi, thus providing valuable genomic information for developing new delousing drugs.

Search for common targets of lithium and valproic acid identifies novel epigenetic effects of lithium on the rat leptin receptor gene.

Epigenetics may have an important role in mood stabilizer action. Valproic acid (VPA) is a histone deacetylase inhibitor, and lithium (Li) may have downstream epigenetic actions. To identify genes commonly affected by both mood stabilizers and to assess potential epigenetic mechanisms that may be involved in their mechanism of action, we administered Li (N = 12), VPA (N = 12), and normal chow (N = 12) to Brown Norway rats for 30 days. Genomic DNA and mRNA were extracted from the hippocampus. We used the mRNA to perform gene expression analysis on Affymetrix microarray chips, and for genes commonly regulated by both Li and VPA, we validated expression levels using quantitative real-time PCR. To identify potential mechanisms underlying expression changes, genomic DNA was bisulfite treated for pyrosequencing of key CpG island 'shores' and promoter regions, and chromatin was prepared from both hippocampal tissue and a hippocampal-derived cell line to assess modifications of histones. For most genes, we found little evidence of DNA methylation changes in response to the medications. However, we detected histone H3 methylation and acetylation in the leptin receptor gene, Lepr, following treatment with both drugs. VPA-mediated effects on histones are well established, whereas the Li effects constitute a novel mechanism of transcriptional derepression for this drug. These data support several shared transcriptional targets of Li and VPA, and provide evidence suggesting leptin signaling as an epigenetic target of two mood stabilizers. Additional work could help clarify whether leptin signaling in the brain has a role in the therapeutic action of Li and VPA in bipolar disorder.

Evaluation of Cellular Proliferative Activity in Patients with Oral Lichen Planus and Hepatitis C through AgNOR Method

The objective of this study was to evaluate the cellular proliferative potential of oral lichen planus (OLP) lesions from patients without hepatitis C virus (HCV) by means of AgNOR method, as well as the cellular proliferative potential of the normal oral mucosa from patients with HCV, treated or untreated by interferon and ribavirin. A cross-sectional study was developed to investigate four groups: 10 HCV+ patients without clinical signs of OLP who had never been treated for HCV infection - Group 1; 10 HCV+ patients that were under interferon and ribavirin treatment - Group 2; 15 patients with reticular OLP lesions histopathologically confirmed, without HCV - Group 3; and 15 blood donors without HCV infection and no clinical signs of OLP GROUP 4 Control Group. The cytological material of all groups was collected by the liquid-based cytology technique. Then, the sedimented material from each patient was filled with the Nucleolar Organizer Regions impregnation by silver method (AgNOR). The count of NORs was performed on 100 epithelial cell nuclei per patient using the Image Tool(tm) software. The Tukey HSD test was used to compare the median value of NORs among the groups and showed that the oral mucosa of HCV+ patients previously treated with anti-HCV drugs (GROUP 2), presented a higher average number of NORs in relation to others (p<0.05). The anti-HCV treatment may be related to increased cell proliferation of oral mucosa, indicating a possible relationship between OLP and HCV+ patients treated with interferon and ribavirin.

O propósito deste estudo foi avaliar o potencial proliferativo celular das lesões de líquen plano bucal (LPB) de pacientes sem vírus da hepatite C (VHC) por meio do método AgNOR, comparando-o ao potencial proliferativo celular da mucosa bucal normal de portadores de VHC, tratados ou não com interferon e ribavirina. Um estudo transversal foi realizado para investigar 4 grupos: 10 pacientes VHC+ sem sinais clínicos de LPB que nunca haviam sido tratados para a infecção por VHC - Grupo 1; 10 pacientes VHC+ que estavam sob tratamento com interferon e ribavirina - Grupo 2; 15 pacientes com LPB reticular histopatologicamente confirmado, sem VHC - Grupo 3; e 15 doadores de sangue sem infecção por VHC e sem sinais clínicos de LPB (Grupo 4 - Grupo de Controle). O material celular de todos os grupos foi coletado pela técnica da citologia em base líquida. Então, o material sedimentado de cada paciente foi submetido ao método da impregnação das regiões organizadoras nucleolares pela prata (AgNOR). A contagem das NORs foi realizada em 100 núcleos celulares epiteliais por paciente por meio do programa Image Tool(r). O teste Tukey HSD foi utilizado para comparar o valor médio de NORs entre os grupos e mostrou que a mucosa bucal dos pacientes VHC+ previamente tratados com fármacos anti-VHC (Grupo 2) apresentou maior número médio de NORs por núcleo em relação aos outros (p<0,05). O tratamento anti-VHC pode estar relacionado ao aumento da atividade proliferativa celular da mucosa bucal, aventando uma possível relação entre LPB e pacientes VHC+ tratados com interferon e ribavirina.

The roles of traditional Chinese medicine in gene therapy.

The field of gene therapy has been increasingly studied in the last four decades, and its clinical application has become a reality in the last 15 years. Traditional Chinese medicine (TCM), an important component of complementary and alternative medicine, has evolved over thousands of years with its own unique system of theories, diagnostics and therapies. TCM is well-known for its various roles in preventing and treating infectious and chronic diseases, and its usage in other modern clinical practice. However, whether TCM can be applied alongside gene therapy is a topic that has not been systematically examined. Here we provide an overview of TCM theories in relation to gene therapy. We believe that TCM theories are congruent with some principles of gene therapy. TCM-derived drugs may also act as gene therapy vehicles, therapeutic genes, synergistic therapeutic treatments, and as co-administrated drugs to reduce side effects. We also discuss in this review some possible approaches to combine TCM and gene therapy.

The anti-tumor drug bleomycin preferentially cleaves at the transcription start sites of actively transcribed genes in human cells.

The genome-wide pattern of DNA cleavage at transcription start sites (TSSs) for the anti-tumor drug bleomycin was examined in human HeLa cells using next-generation DNA sequencing. It was found that actively transcribed genes were preferentially cleaved compared with non-transcribed genes. The 143,600 identified human TSSs were split into non-transcribed genes (82,596) and transcribed genes (61,004) for HeLa cells. These transcribed genes were further split into quintiles of 12,201 genes comprising the top 20, 20-40, 40-60, 60-80, and 80-100 % of expressed genes. The bleomycin cleavage pattern at highly transcribed gene TSSs was greatly enhanced compared with purified DNA and non-transcribed gene TSSs. The top 20 and 20-40 % quintiles had a very similar enhanced cleavage pattern, the 40-60 % quintile was intermediate, while the 60-80 and 80-100 % quintiles were close to the non-transcribed and purified DNA profiles. The pattern of bleomycin enhanced cleavage had peaks that were approximately 200 bp apart, and this indicated that bleomycin was identifying the presence of phased nucleosomes at TSSs. Hence bleomycin can be utilized to detect chromatin structures that are present at actively transcribed genes. In this study, for the first time, the pattern of DNA damage by a clinically utilized cancer chemotherapeutic agent was performed on a human genome-wide scale at the nucleotide level.

Aspirin exposure reveals novel genes associated with platelet function and cardiovascular events.

OBJECTIVES: The aim of this study was to develop ribonucleic acid (RNA) profiles that could serve as novel biomarkers for the response to aspirin. BACKGROUND: Aspirin reduces death and myocardial infarction (MI), suggesting that aspirin interacts with biological pathways that may underlie these events. METHODS: Aspirin was administered, followed by whole-blood RNA microarray profiling, in a discovery cohort of healthy volunteers (HV1) (n = 50) and 2 validation cohorts of healthy volunteers (HV2) (n = 53) and outpatient cardiology patients (OPC) (n = 25). Platelet function was assessed using the platelet function score (PFS) in HV1 and HV2 and the VerifyNow Aspirin Test (Accumetrics, Inc., San Diego, California) in OPC. Bayesian sparse factor analysis identified sets of coexpressed transcripts, which were examined for associations with PFS in HV1 and validated in HV2 and OPC. Proteomic analysis confirmed the association of validated transcripts in platelet proteins. Validated gene sets were tested for association with death or MI in 2 patient cohorts (n = 587 total) from RNA samples collected at cardiac catheterization. RESULTS: A set of 60 coexpressed genes named the "aspirin response signature" (ARS) was associated with PFS in HV1 (r = -0.31, p = 0.03), HV2 (r = -0.34, Bonferroni p = 0.03), and OPC (p = 0.046). Corresponding proteins for the 17 ARS genes were identified in the platelet proteome, of which 6 were associated with PFS. The ARS was associated with death or MI in both patient cohorts (odds ratio: 1.2 [p = 0.01]; hazard ratio: 1.5 [p = 0.001]), independent of cardiovascular risk factors. Compared with traditional risk factors, reclassification (net reclassification index = 31% to 37%, p ≤ 0.0002) was improved by including the ARS or 1 of its genes, ITGA2B. CONCLUSIONS: RNA profiles of platelet-specific genes are novel biomarkers for identifying patients who do not respond adequately to aspirin and who are at risk for death or MI.