Genome Analysis Techniques Research Articles

Noncoding RNAs and Its Implication as Biomarkers in Renal Cell Carcinoma: A Systematic Analysis

Renal cell carcinoma (RCC) is one of the most devastating disease with higher mortality rates. It comprises several subtypes exhibiting distinct histological features and clinical staging. Despite recent advancement in understanding the biology of RCC success in treatment rates remains dismal. This may be partly due to lack of specific biomarkers for early detection/prognosis and poor clinical outcome. Noncoding protein transcripts in the genome play important role in the initiation, evolution and progression of cancer. With the advancement in genomic analysis techniques, especially next-generation sequencing, a large number of new transcripts have been discovered, leading to better understanding of coding and noncoding RNAs. In the present review, we summarize recent advancement on renal cancer associated noncoding RNAs which includes long noncoding RNAs, microRNAs, and circular RNAs for their involvement in RCC along with their clinical implication as prognostic and diagnosis biomarkers.

The Cancer Genome Atlas Project in Bladder Cancer.

Bladder cancer (BC) remains an aggressive disease with a poor prognosis, especially for patients with metastatic disease who have a limited median overall survival of 14months. Urothelial carcinomas harbor frequent molecular dysregulations including recurrent mutations and copy number alteration, some of which could be potential therapeutic targets. However, no molecularly targeted agents have been approved to date for the treatment of advanced BC. Gaining new insights into the molecular landscape of BC will be critical to tailor future targeted agents for the treatment of advanced disease. The Cancer Genome Atlas (TCGA) project is cataloguing the genetic and epigenetic alterations responsible for cancer through the application of high-throughput genome analysis techniques. After the landmark paper profiling 131 patients was published in 2014, additional patients have been added with an updated TCGA analysis now including 412 patients. This chapter will review the previously described genomic alterations reported in the first manuscript and the new major highlights found in the expanded analyses recently published. The aim will be to review how this comprehensive integrated genomic analysis can inform the design of precision medicine targeted therapy for the treatment of advanced disease.

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA).

Coronaviruses are of major importance for both animal and human health. With the emergence of novel coronaviruses such as SARS and MERS, the need for fast genome characterisation is ever so important. Further, in order to understand the influence of quasispecies of these viruses in relation to biology, techniques for deep-sequence and full-length viral genome analysis are needed. In the present study, we compared the efficiency of two sequence-independent approaches [sequence-independent single primer amplification (SISPA) and single primer isothermal amplification (SPIA, represented by the Ovation kit)] coupled with high-throughput sequencing to generate the full-length genome of bovine coronavirus (BCoV) from a nasal swab. Both methods achieved high genome coverage (100% for SPIA and 99% for SISPA), however, there was a clear difference in the percentage of reads that mapped to BCoV. While approximately 45% of the Ovation reads mapped to BCoV (sequence depth of 169–284 944), only 0.07% of the SISPA reads (sequence depth of 0–249) mapped to the reference genome. Although BCoV was the focus of the study we also identified a bovine rhinitis B virus (BRBV) in the data sets. The trend for this virus was similar to that observed for BCoV regarding Ovation vs. SISPA, but with fewer sequences mapping to BRBV due to a lower amount of this virus. In summary, the SPIA approach used in this study produced coverage of the entire BCoV (high copy number) and BRBV (low copy number) and a high sequence/genome depth compared to SISPA. Although this is a limited study, the results indicate that the Ovation method could be a preferred approach for full genome sequencing if a low copy number of viral RNA is expected and if high sequence depth is desired.

Investigating the Biosynthesis of Natural Products from Marine Proteobacteria: A Survey of Molecules and Strategies.

The phylum proteobacteria contains a wide array of Gram-negative marine bacteria. With recent advances in genomic sequencing, genome analysis, and analytical chemistry techniques, a whole host of information is being revealed about the primary and secondary metabolism of marine proteobacteria. This has led to the discovery of a growing number of medically relevant natural products, including novel leads for the treatment of multidrug-resistant Staphylococcus aureus (MRSA) and cancer. Of equal interest, marine proteobacteria produce natural products whose structure and biosynthetic mechanisms differ from those of their terrestrial and actinobacterial counterparts. Notable features of secondary metabolites produced by marine proteobacteria include halogenation, sulfur-containing heterocycles, non-ribosomal peptides, and polyketides with unusual biosynthetic logic. As advances are made in the technology associated with functional genomics, such as computational sequence analysis, targeted DNA manipulation, and heterologous expression, it has become easier to probe the mechanisms for natural product biosynthesis. This review will focus on genomics driven approaches to understanding the biosynthetic mechanisms for natural products produced by marine proteobacteria.

209 Evaluation of acute cardiac damage in a porcine model of defibrillation

IntroductionTransthoracic defibrillation is performed to correct life threatening cardiac arrhythmias of the heart, i.e. ventricular fibrillation (VF) and ventricular tachycardia (VT). These are due to chaotic electrical excitation of the...

Why were Sardinians the shortest Europeans? A journey through genes, infections, nutrition, and sex.

Since ancient times the Mediterranean island of Sardinia has been known for harboring a population with an average body height shorter than almost every other ethnic group in Europe. After over a century of investigations, the cause(s) at the origin of this uniqueness are not yet clear. The shorter stature of Sardinians appears to have been documented since prehistoric times, as revealed by the analysis of skeletal remains discovered in archaeological sites on the island. Recently, a number of genetic, hormonal, environmental, infective and nutritional factors have been put forward to explain this unique anthropometric feature, which persisted for a long time, even when environmental and living conditions improved around 1960. Although some of the putative factors are supported by sound empirical evidence, weaker support is available for others. The recent advent of whole genome analysis techniques shed new light on specific variants at the origin of this short stature. However, the marked geographical variability of stature across time and space within the island, and the well-known presence of pockets of short height in the population of the southern districts, are still puzzling findings that have attracted the interest of anthropologists and geneticists. The purpose of this review is to focus on the state-of-the-art research on stature, as well as the factors that made Sardinians the shortest among Europeans.

Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

BackgroundPhage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes.ResultsThe original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome.ConclusionsUsing available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3018-2) contains supplementary material, which is available to authorized users.

Genetic and environmental risk factors for atherosclerosis regulate transcription of phosphatase and actin regulating gene PHACTR1

Background and aimsCoronary artery disease (CAD) risk is associated with non-coding genetic variants at the phosphatase and actin regulating protein 1(PHACTR1) gene locus. The PHACTR1 gene encodes an actin-binding protein with phosphatase regulating activity. The mechanism whereby PHACTR1 influences CAD risk is unknown. We hypothesized that PHACTR1 would be expressed in human cell types relevant to CAD and regulated by atherogenic or genetic factors. Methods and resultsUsing immunohistochemistry, we demonstrate that PHACTR1 protein is expressed strongly in human atherosclerotic plaque macrophages, lipid-laden foam cells, adventitial lymphocytes and endothelial cells. Using a combination of genomic analysis and molecular techniques, we demonstrate that PHACTR1 is expressed as multiple previously uncharacterized transcripts in macrophages, foam cells, lymphocytes and endothelial cells. Immunoblotting confirmed a total absence of PHACTR1 in vascular smooth muscle cells. Real-time quantitative PCR showed that PHACTR1 is regulated by atherogenic and inflammatory stimuli. In aortic endothelial cells, oxLDL and TNF-alpha both upregulated an intermediate length transcript. A short transcript expressed only in immune cells was upregulated in macrophages by oxidized low-density lipoprotein, and oxidized phospholipids but suppressed by lipopolysaccharide or TNF-alpha. In primary human macrophages, we identified a novel expression quantitative trait locus (eQTL) specific for this short transcript, whereby the risk allele at CAD risk SNP rs9349379 is associated with reduced PHACTR1 expression, similar to the effect of an inflammatory stimulus. ConclusionsOur data demonstrate that PHACTR1 is a key atherosclerosis candidate gene since it is regulated by atherogenic stimuli in macrophages and endothelial cells and we identify an effect of the genetic risk variant on PHACTR1 expression in macrophages that is similar to that of an inflammatory stimulus.

Conservation of Genetic Diversity: It's Relevance in Poultry Production

Genetic diversity refers to the total number of genetic characteristics in the genetic make-up of a species. It shows variation that exists between breeds of the same species. Genetic diversity serves as a way for populations to adapt to changing environment. An increasing loss of genetic diversity has been observed for all agriculturally used species and poultry genetic resources are considered to be the most endangered. Selective breeding by humans has led to the creation of many breeds characterized by high productivity, leading to the displacement of local breeds and posing a threat to the survival of many native breeds. Genetic resources are the building blocks for poultry development. The relevance of genetic diversity conservation in poultry production cannot be overemphasized because genes play a major role in formation of breeds and species. With recent advances in molecular technology, a number of techniques for in-depth genome analysis and evaluation of genetic variation in different breeds of poultry have been developed.

Abstract 52: QDNAseq: A bioinformatics pipeline for DNA copy number analysis from shallow whole genome sequencing with noise levels near the probabilistic lower limit imposed by read counting

Abstract The emerging field of precision medicine considers the patient's individual genetic make up, environment, and lifestyle to arrive at individualized treatment. For cancer patients, analysis of the tumour genome can reveal actionable alterations, including mutations (e.g., BRAF mutation in melanoma), translocations (e.g., t(9;22)(q34;q11) in CML) and copy number changes (e.g., HER2 amplification in breast cancer). Formalin-fixed paraffin embedded (FFPE) biopsy or surgical pathology samples are often the only materials available for analysis, highlighting the need for genomic analysis techniques that perform reliably with such materials. We present a complete pipeline for DNA copy number profiling by sequencing called quantitative DNA sequencing (QDNAseq), which offers a cost effective procedure for genome-wide DNA copy number analysis, facilitates correct biological interpretations from samples with a varying range of quality and is suitable for routine pathology diagnostics from fresh, frozen and FFPE materials. QDNAseq is implemented in R and made available through BioConductor and Galaxy. The pipeline requires as little as ∼0.1× genome coverage (∼6 million single-end 50nt reads per sample) and utilizes a depth of coverage (DOC) approach. A two-dimensional LOESS correction is applied for GC content and mappability and data from the 1000 genomes project are used to compile a blacklist of problematic genome regions. Downstream analyses have been included in QDNAseq by adapting algorithms previously developed for segmentation (DNAcopy) and the calling of gains and losses (CGHcall). QDNAseq is able to produce profiles with noise levels near the probabilistic lower limit imposed by read counting and yields a higher resolution than is available from microarrays. Some samples, however, have variances clearly above the probabilistic lower limit and are characterized by a wave pattern. This pattern originates in the sample, as it is reproducible, both in magnitude and in shape along the genome. Much of this wave bias can be reduced by regression with profiles from matched normal FFPE DNA samples using the algorithm implemented in NoWaves. The QDNAseq procedure is highly cost effective and robust. We have processed over 1500 clinical samples obtained from the FFPE archives of more than 25 institutions from Europe and North America. Citation Format: Daoud Sie, Ilari Scheinin, Stef Lieshout, van, Martijn Cordes, Daniel Pinkel, Donna G. Albertson, Mark A. Wiel, van de, Bauke Ylstra. QDNAseq: A bioinformatics pipeline for DNA copy number analysis from shallow whole genome sequencing with noise levels near the probabilistic lower limit imposed by read counting. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 52.

Molecular pathogenesis of peripheral T cell lymphoma (2): extranodal NK/T cell lymphoma, nasal type, adult T cell leukemia/lymphoma and enteropathy associated T cell lymphoma

Peripheral T-cell lymphomas (PTCL) belong to the group of non-Hodgkin lymphoma and particularly that of mature T /NK cells lymphoproliferative neoplasms. The 2008 WHO classification describes different PTCL entities with varying prevalence. With the exception of histologic subtype "ALK positive anaplastic large cell lymphoma", PTCL are characterized by a poor prognosis. The mechanisms underlying the pathogenesis of these lymphomas are not yet fully understood, but development of genomic high-throughput analysis techniques now allows to extensively identify the molecular abnormalities present in tumor cells. This review aims to summarize the current knowledge and recent advances about the molecular events occurring at the origin or during the natural history of main entities of PTCL. The first part published in the October issue was focused on the three more frequent entities, i.e. angioimmunoblastic T-cell lymphoma, peripheral T-cell lymphoma, not otherwise specified, and anaplastic large cell lymphoma. The second part presented herein will describe other subtypes less frequent and of poor prognosis : extranodal NK/T-cell lymphoma, nasal type, adult T-cell leukemia/lymphoma, and enteropathy-associated T-cell lymphoma.

Molecular pathogenesis of peripheral T-cell lymphoma (1): angioimmunoblastic T-cell lymphoma, peripheral T-cell lymphoma, not otherwise specified and anaplastic large cell lymphoma

Peripheral T-cell lymphomas (PTCL) belong to the group of non-Hodgkin lymphoma and particularly that of mature T/NK cells lymphoproliferative neoplasms. The 2008 WHO classification describes different PTCL entities with varying prevalence. With the exception of the histological subtype "ALK positive anaplastic large cell lymphoma", PTCL are characterized by a poor prognosis. The mechanisms underlying the pathogenesis of these lymphomas are not yet fully understood, but development of genomic high-throughput analysis techniques now allows to extensively identify the molecular abnormalities present in tumor cells. This review aims to summarize the current knowledge and recent advances about the molecular events occurring at the origin or during the natural history of main entities of PTCL. It will be published in two parts: the first is focused on the three more frequent entities, angioimmunoblastic T-cell lymphoma, peripheral T-cell lymphoma, not otherwise specified, and anaplastic large cell lymphoma. The second (which will appear in the november issue) will describe other subtypes less frequent and of poor prognosis: extranodal NK/T-cell lymphoma, nasal type, adult T-cell leukemia/lymphoma, and enteropathy-associated T-cell lymphoma. T or NK cell lymphoproliferative disorders with leukemic presentation, primary cutaneous T-cell lymphoma and very rare subtypes of PTCL whose prevalence is less than 5% (hepatosplenic T-cell lymphoma and subcutaneous panniculitis-like T cell lymphoma) will not be discussed herein.

Investigating Physical Chromatin Associations Across the Xenopus Genome by Chromatin Immunoprecipitation

Chromatin immunoprecipitation (ChIP) combined with genomic analysis techniques provide a global snapshot of protein-DNA interactions in the context of chromatin, yielding insights into which genomic loci might be regulated by the DNA-associated protein under investigation. This protocol describes how to perform ChIP on intact or dissected Xenopus embryos. The ChIP-isolated DNA fragments are suitable for high-throughput sequencing (ChIP-Seq) or for quantitative PCR (ChIP-qPCR). In this protocol, embryonic tissue is harvested from Xenopus tropicalis or Xenopus laevis at the developmental stage of interest, and DNA-associated proteins are immobilized to their endogenous genomic binding sites with formaldehyde. Nuclei are extracted from embryos and subjected to sonication so as to shear the chromatin to a size that allows sufficient positional resolution of protein binding to genomic DNA. Chromatin fragments bound by the protein of interest are immunoprecipitated using antibody-coupled beads, washed under high-stringency conditions, and stripped from the beads with anionic detergents. The chemical cross-links are reversed, and the coimmunoprecipitated DNA is purified. The resulting DNA fragments can be analyzed by qPCR or used to create a ChIP-Seq library. General advice for qPCR and for making ChIP-Seq libraries is offered, and approaches for analyzing ChIP-Seq data are outlined.

Therapeutic Peptides: New Arsenal Against Drug Resistant Pathogens

Our incessant tug-of-war with multidrug resistant pathogenic bacteria has prompted researchers to explore novel methods of designing therapeutics in order to defend ourselves against infectious diseases. Combined advances in whole genome analysis, bioinformatics algorithms, and biochemical techniques have led to the discovery and subsequent characterization of an abundant array of functional small peptides in microorganisms and multicellular organisms. Typically classified as having 10 to 100 amino acids, many of these peptides have been found to have dual activities, executing important defensive and regulatory functions in their hosts. In higher organisms, such as mammals, plants, and fungi, host defense peptides have been shown to have immunomodulatory and antimicrobial properties. In microbes, certain growth-inhibiting peptides have been linked to the regulation of diverse cellular processes. Examples of these processes include quorum sensing, stress response, cell differentiation, biofilm formation, pathogenesis, and multidrug tolerance. In this review, we will present a comprehensive overview of the discovery, characteristics, and functions of host- and bacteria-derived peptides with antimicrobial activities. The advantages and possible shortcomings of using these peptides as antimicrobial agents and targets will also be discussed. We will further examine current efforts in engineering synthetic peptides to be used as therapeutics and/or drug delivery vehicles.

TopFed: TCGA tailored federated query processing and linking to LOD.

BackgroudThe Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis.MethodsWe address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed.ResultsWe compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX.ConclusionWith TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and parsing.

Ocena znaczenia klinicznego submikroskopowych duplikacji chromosomowych u pacjentów z opóźnieniem rozwoju i cechami dysmorfii

IntroductionChromosomal microaberrations are considered to be one of the most common causes of psychoneurological disability, if it coexists with congenital malformations and/or dysmorphic features. Autosomal duplications produce partial trisomies (covering the defined parts of the genome) with which phenotypic abnormalities are often associated. With new, high-resolution methods of molecular karyotyping it is possible to identify chromosomal microaberrations of several hundred thousand base pairs. AimsStudy aims to show diagnostic difficulties in demonstrating the correlation between the phenotype and chromosomal abnormalities, based on an example of 7 patients. Material and methodsThe study included a group of 7 children (2 girls and 5 boys). Classical methods of karyotyping, the microarray CGH (aCGH) and FISH with locus-specific probes techniques were used to analyze the genome. ResultsMicroduplications found in patients were divided into three different categories, reflecting their presumed clinical significance:1.Pathogenic aberrations.2.Presumably pathogenic aberrations.3.Aberrations with clinical significance currently impossible to interpret.In case of patients with localized submicroscopic chromosomal microduplications there was an attempt to identify the genes contained therein, based on available chromosome maps. ConclusionsThe explanation of the genetic basis of phenotypic abnormalities ascertained in patients with an abnormal karyotype is a multistep process and requires the use of various techniques for genome analysis. The evaluation of microduplications’ clinical significance is complicated due to very few reports of such syndromes as well as only a few molecular studies on the functions and interactions of expression products of genes in the area of chromosomal rearrangement.

SAT0079 The analysis of fecal microbiota in rheumatoid arthritis patients compared to healthy volunteers using bacterial RRNA-targeted reverse transcription-quantitative PCR

BackgroundGut microbiota have long been thought to contribute to inflammatory disease, and some have considered the bacterial flora as one of the environmental factors causing rhumatoid arthritis (RA). Recently, two...

Abstract 5310: Regulation of metastatic breast cancer by E2F transcription factors

Abstract Metastasis is the leading cause of mortality in breast cancer and the purpose of this study was to examine the role of the E2F transcription factors in mediating the dissemination of the primary cancer. E2F transcription factors have previously been demonstrated to play a critical role in regulation of cell cycle progression. However, in prior work we have demonstrated that gene expression signatures for the E2Fs have variable levels of activation in a heterogeneous tumor model. Using predictive bioinformatic methods to assess the probability of gene pathway activation, we have predicted variable roles for the E2Fs in key mouse models of breast cancer, including Myc, PyMT and Neu. We then genetically tested these computational predictions by interbreeding E2F knockout mice to the various transgenic tumor models. These crosses have revealed that the E2Fs have unique roles in tumor initiation and progression depending upon the oncogene driving the initial tumor. There are differential effects on tumor latency with the loss of individual E2F alleles, including decreased latency with E2F2 loss in the PyMT background but increased latency and reduced incidence in the Myc background. Moreover, we have observed key differences in tumor progression, with loss of E2Fs affecting the heterogeneity of the resulting tumors. In addition to tumor initiation, we have observed striking differences in tumor progression with loss of E2Fs increasing metastasis in the Myc model but reducing metastasis in the PyMT model. In order to determine the mechanism of action for these effects, we have undertaken a gene expression analysis from both primary tumors and the metastases. Comparison of tumor models in the various backgrounds has allowed us to generate a list of E2F target genes that have effects on metastasis. Comparison of these genes to human breast cancer has revealed that the key genes also have critical roles in metastatic human breast cancer survival. These E2F targets include genes that have previously been identified as metastasis suppressors and are being validated in this process. Taken together, this work suggests a critical role for the E2F transcription factors, not only as mediators of cell cycle but in regulating the metastatic progression of metastatic breast cancer. These data also illustrate the power of combining various genomic and gene expression analysis techniques with both mouse models and clinical data associated with gene expression analysis in human breast cancer. Using this approach we are able to predict and test for the role of critical pathways, such as the E2Fs, in the progression of breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5310. doi:1538-7445.AM2012-5310

Abstract P146: Fas-ligand Induces Cardiomyopathy via the Activation of the Erk1/2 Pathway

Fas receptor and its ligand, Fas-L, are the most well characterized co-stimulatory molecules playing an essential role in the induction of programmed cell death or apoptosis. Increase of circulating Fas-L in serum and in cardiomyocytes are described in different models of cardiac diseases such as myocarditis, pressure overload, AND myocardial infarction/ischemia. In addition, associated activation of inflammatory pathwayshas been observed. However, no studies have yet revealed mechanisms underlying the pathogenecity of FasL in the heart. Transgenic mice (C57/Bl6) with cardiac-specific over-expression of Fas-L were investigated. We characterized cardiac function by echocardiography. Cellular and molecular studies were performed on heart tissue using genomic, histologic, immunological, and protein analysis techniques. Fas-L transgenic mice had a significant rate of mortality (p<0.0001) compared to WT due to heart failure. Histological studies of Fas-L hearts revealed predominant perivascular fibrosis associated with inflammation. Expression studies of secondary messengers of the activated Fas/FasL system demonstrated up-regulation of an active CASP-3 confirming induction of apoptosis in myocardium. Down-regulation of FLIP, NIK and NF-κB was evident. Interestingly, RIP was up-regulated leading to the activation of ERK1/2 (4.27±0.158 vs 10.086±1.591 in WT and FasL mice hearts, respectively, p=0.022). Analysis of inflammatory mediators revealed increase in secretion of interleukines (IL-17, IL-6, IL-1β and TNF-α) and diffuse infiltration of CD3 positive cells. Studies of fibrotic pathways showed an increased expression of periostin and osteopontin, but not activation of TGFβ1, showing that periostin and osteopontin can be activated independently of TGFβ1 via the ERK1/2 pathway, Our findings suggest that Fas-L induces cardiac failure, via an activation of the ERK1/2 pathway, which is an important player involved in the hypertrophic response in the heart. Targeting the ERK1/2 pathway in cardiac diseases associated with Fas-L expression may therefore be able to prevent progression to cardiomyopathy.

Toward understanding genetic risk for differential antipsychotic response in individuals with schizophrenia

Antipsychotic treatment response is highly heterogeneous and unpredictable in terms of both efficacy and side effects. A combination of factors influences treatment outcome, including clinical, demographic, environmental and genetic factors. No comprehensive studies have quantified the relative contributions of these factors to date. Two decades of pharmacogenetic and pharmacogenomic studies have attempted to identify key gene variants associated with antipsychotic response, with a dual goal of better understanding the mechanisms underlying drug response and guiding prescribing decisions in clinical care. Pharmacogenetic studies have succeeded in identifying several genes that are associated with antipsychotic treatment efficacy or side effects. However, the strength of these associations is modest and they are of limited clinical value. Genome-wide association studies, moving beyond hypothesis-based discovery, have greater potential to identify novel gene associations, although only a few genome-wide association studies have been conducted and they have not revealed clearly significant findings. The first pharmacogenetic tests to guide the selection or dosing of antipsychotic drugs are now commercially available. Their uptake has been limited by the modest level of prediction they offer, compounded by the lack of data supporting their clinical or economic benefits. Advances in genomic analysis techniques, the better characterization of larger subject cohorts and an improved understanding of the role of environmental factors and gene–environment interactions are renewing hope that future research will identify genetic variants with stronger associations with treatment outcome. Tests incorporating such genetic data, with environmental and clinical variables, may offer the potential to personalize medicine and significantly improve the efficacy and tolerability of antipsychotic treatment.