Caenorhabditis elegans as a novel model system for studying these effects.Highly active antiretroviral therapy (HAART) has significantly increased life expectancy of the human immunodeficiency virus (HIV)-positive population. Nevertheless, the average lifespan of HIV-patients remains shorter compared to uninfected individuals. Immunosenescence, a current explanation for this difference invokes heavily on viral stimulus despite HAART efficiency in viral suppression. We propose here that the premature and accelerated aging of HIV-patients can also be caused by adverse effects of antiretroviral drugs, specifically those that affect the mitochondria. The nucleoside reverse transcriptase inhibitor (NRTI) antiretroviral drug class for instance, is known to cause depletion of mitochondrial DNA via inhibition of the mitochondrial specific DNA polymerase-γ. Besides NRTIs, other antiretroviral drug classes such as protease inhibitors also cause severe mitochondrial damage by increasing oxidative stress and diminishing mitochondrial function. We also discuss important areas for future research and argue in favor of the use of  Retrovirus of the Lentivirus genus that primarily infects cells of the host immune system. Once an individual is infected, HIV-1 replication takes place in several steps. In the first step, the virion attaches itself to the host cell with the help of co-receptors, whereupon it fuses with the host cell membrane and the two single-stranded RNA molecules and three different viral enzymes are released into the host cell cytoplasm. The viral reverse transcriptase transcribes the viral RNA into DNA, at which point the viral DNA is transported into the nucleus. With the aid of the viral integrase the viral DNA is processed and incorporated into the host genome. The integrated viral DNA, now known as a provirus, is transcribed and translated by the host machinery to synthesize viral proteins and single-stranded RNA for new virions. After assembly of these components at the plasma membrane, the new virions bud off and mature using the viral protease, completing the HIV-1 life cycle  is a e Figure . HIV infFigure 1), and are used in unison to increase therapy efficacy, overcome problems of tolerance, and decrease emergence of viral resistance. The major classes include the entry inhibitors (EIs), the nucleoside reverse transcriptase inhibitors (NRTIs), the non-nucleoside reverse transcriptase inhibitors (NNRTIs), and the protease inhibitors (PIs). The additional two anti-HIV drug classes are the maturation inhibitors (MIs) and integrase inhibitors (IIs), of which most compounds are still in clinical development.For the treatment of HIV-1 infection there are currently six different classes of anti-HIV drugs. Each class of drug acts on a particular aspect of the viral life cycle (Table 1) and often supplemented with one drug from another class . Due to the large variety in drug combinations, standard HAART has been defined as one or more NRTIs combined with a PI  homeostasis. Therefore, a perturbation of any of these functions impairs cellular life-expectancy and has been shown to have tissue and systemic repercussions including accelerated aging . In consBecause mitochondria contain their own DNA, mitochondrial genome integrity is essential for organelle function. The mtDNA encodes vital components of the mitochondrial respiratory chain and therefore damage to mtDNA is directly detrimental to energy metabolism and organelle fitness. Not surprisingly, cell senescence and aging are associated with an increase in the amount of damaged mtDNA. Additionally, accumulation of mutations in mtDNA is known to increase with age, and aberrant mtDNA replication contributes to premature-and-accelerated-aging phenotypes .Figure 2; alovudine or FLT), known for its high toxicity, can cause DNA fragmentation and induce apoptosis (zidovudine or AZT) and 2′,3′-didehydro-2′,3′-deoxythymidine (stavudine or d4T) also disrupt telomerase maintenance and have telomere shortening effects, properties often related to cell senescence and aging  is used in the HAART cocktail. RTV impedes the enzyme cytochrome P450-CYP3A4, which is responsible for the metabolism of xenobiotics, and therefore RTV induces an increase in intracellular drug concentrations in the patient  induced ROS production, independent of mtDNA depletion or damage, a finding that emphasizes the impact of antiretroviral-induced ROS toxicity , two frequently prescribed PIs, can increase ROS production in human arterial endothelial cells (Indinavir (IDV) and nelfinavir (NFV) have been shown to elicit ROS production in skin fibroblast cultures in vitro and in patients’ adipose tissue in vivo (Saquinavir (SQV) however, was shown to cause apoptosis in human umbilical vein endothelial cells via higher levels of ROS production -treated human hepatocytes show widespread mitochondrial swelling with poorly organized cristae . C. elegans demonstrated that NRTIs decrease mtDNA copy number, disrupt both structure and function of mitochondria and shorten the average lifespan. Using oxygen consumption as a measure of mitochondrial function, NRTIs were shown to induce a rapid decrease in mitochondrial fitness. These findings compare well to earlier studies wherein abnormal mitochondrial respiratory activity was correlated with altered expression or deficiency in various respiratory chain complexes .omplexes . AdditioFigure 3). However, there are a number of questions that remain unanswered, simply because we do not fully understand the effects of antiretroviral drugs individually, let alone in combination.With the increase in life expectancy it has only recently become clear that HIV-1 patients are suffering from symptoms of aging ahead of time. In this review we postulate that strong correlations exist between antiretroviral drug-induced mitochondrial toxicity and premature and accelerated aging (For example, questions remain about mitochondrial toxicity of NRTIs beyond the polymerase-γ theory. Various cellular transport systems interact with NRTIs and once inside the cell NRTIs are actively phosphorylated from their pro-drug form . ChangesC. elegans as a model system to study the effects of antiretroviral therapy on premature and accelerated aging. Using C. elegans we can begin to study the effects of specific genetic backgrounds on HAART toxicities. Effects of HAART seen in the nematode can direct more specific research into human conditions. In addition, C. elegans could provide an easy platform, not just for toxicity studies of various antiretroviral drugs, but also to screen for suitable compounds that neutralize toxic effects of HAART, which remains crucial as long as total HIV eradication is not possible. Combining these genetic and toxicology approaches we can initiate research leading to efficient, personalized, anti-HIV treatment in humans.We propose the use of The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Men with metastatic castration-resistant prostate cancer (mCRPC) carry poor prognosis despite the use of docetaxel-based regimens which has modest survival benefit shown by randomized clinical trials. Significant progress in the discovery of novel therapeutic agents has been made in the past few years. While sipuleucel-T, cabazitaxel, and abiraterone gained regulatory approval in 2010 and 2011, several highly promising candidates/regimens have failed in large scale clinical trials. Challenges remain to optimize the design and interpretation of clinical trial results and develop more effective strategies for mCRPC. In this review, we examined the positive and negative clinical trials in mCRPC in the past and discussed the various aspects of clinical trial design including selection of targets and appropriate outcome measures, biomarker development and implementation, and strategies for combination therapy. Prostate cancer is the most common non-cutaneous malignancy and the second leading cause of cancer deaths among men in the United States, with an estimated incidence of 241,740 new cases diagnosed and approximately 28,170 men expected to die of the disease in 2012 . The resHER-2 positive breast cancer, crizotinib for ALK-mutated lung cancer, and vemurafenib for BRAF-mutated advanced melanoma have all confirmed the significance and feasibility of targeted therapy [Unraveling the molecular make up of cancer cells has resulted in the successful development of specific targeted therapies directed at particular molecular pathways. Studies involving imatinib for CML and GIST, trastuzumab for  therapy . Conside therapy -10. Many therapy ,12.The progression of mCRPC can occur as a result of AR activation despite low levels of androgens. Numerous molecular and genetic aberrations have been postulated to be responsible for gain-of-function changes in the AR signaling pathway under androgen deprivation. This includes intratumoral androgen synthesis, AR protein overexpression, AR gene amplification or point mutations, constitutively active truncated AR splice variants, disturbance of AR-coactivator-corepressor complex, and ligand-independent AR activation by kinase cross-talk ,13. PatiOn the other hand, zibotentan, an endothelin A receptor antagonist blocking endothelin-mediated activation of multiple signaling transduction pathways , showed P = .0077) [Similar disappointing results were reported that led to the termination of the late-stage trial of sunitinib, an antiangiogenic TKI, in combination with prednisone as second-line therapy for mCRPC patients due to the lack of OS prolongation, despite an improvement in progression-free survival (PFS)  . The ini= .0077) ,24. One = .0077) . Some di= .0077) . AnotherWhile recognizing the essential role of early clinical trials in enhancing our understanding of disease biology, we must be conscious about the limitations in interpreting results owing to insufficient sample size, unreliable surrogate markers, or suboptimal outcome measures. Undoubtedly, such trials are required to facilitate efficient screening for active compounds for further clinical development. Selecting appropriate targets for development in phase III trials and the decision to move the drug forward can be difficult at times when early trials reveal only mild clinical activity based on current, suboptimal trial designs. A more stringent and validated benchmark in assessing a meaningful clinical benefit is in enormous demand.The efficient design of phase II trials to identify active compounds for phase III testing remains a challenge. Alternate end points for screening phase II studies are urgently needed to limit the high incidence of negative phase III trials. Choosing the most suitable primary endpoints for prostate cancer trials has been challenging historically. Although OS is the gold standard for demonstrating clinical benefit due to its objectivity, it requires larger patient numbers and longer follow-up. Survival analysis may also be confounded by crossover or subsequent therapies administered after a study drug is discontinued. Valid intermediate surrogate endpoints have been the center of debate for the past few years. Analyses of PSA response rates, objective response rates and PFS have all been proposed as means to accelerate the drug development process.Most phase II trials have used PSA decline of more than 50 percent as the primary endpoint, based on its high predictive value of survival from a multivariate analysis  and the Response rates have also been assessed in patients with measureable diseases on CT scans. However, the clinical picture of mCRPC is dominated by bone metastases in 90-95% of the patients. Radionuclide bone scan is routinely used to assess these bony lesions but the criteria for response categorization are not well-defined and reported in clinical trials. Other imaging modalities (MRI and PET) to assess bone metastasis are still under investigation . MoreoveWhether PFS is a justifiable intermediate surrogate endpoint in prostate cancer is still an open question. PFS is defined as the time from study entry or randomization of a patient until objective tumor progression or death. The use of PFS in trials has several advantages that include a smaller sample size and shorter duration of follow-up. PFS is also not affected by crossover or subsequent treatments. Various definitions for PFS, including PSA, radiographic changes, new metastatic lesions, and disease-related symptoms, have been used in clinical practice. However, data has shown that current measures of PFS for men with CRPC are not strong surrogates for OS ,36. It aGiven that there are no validated surrogates of OS to assess early clinical benefit in CRPC trials, incorporation of relevant biomarkers in early phases of clinical development is essential to improve the success of late phase III testing. Clinical trial design is challenged by the ability to correlate clinical outcome with specific biomarkers reflective of the tumor phenotype with predictive or prognostic value. PSA has long been used as prognostic marker but due to its limitations, various PSA-based biomarkers were explored such as PSA velocity, PSA doubling time, etc. A systematic review of the literature highlighted conflicting data from heterogeneous studies on the use of such biomarkers as prognostic risk factors;  thus, thETS fusions with TMPRSS2 as the first recurrent genomic alteration in prostate cancer. The ETS-related gene (ERG) is the most common fusion partner for the androgen-regulated gene TMPRSS2[ETS fusion-positive prostate cancer usually carries a more aggressive phenotype but still respond to ADT owing to its 5’ androgen-regulated partner, makes it an ideal potential predictive biomarker for ADT. In fact, increased prevalence of patients with hormone-regulated ERG gene rearrangement was identified in a group of mCRPC patients treated with AA who had more than 90% PSA declines [TMPRSS2-ERG fusion status in patients enrolled in sequential phase II AA trials, similar rate of PSA response were indentified in both groups regardless of the presence of TMPRSS2-ERG fusion. Thus, the predictive value of TMPRSS2-ERG for the response to hormonal treatment is still uncertain at this time. Moreover, it has been technically challenging in developing inhibitors of ETS fusions targeting the 3’ ETS due to its poor accessibility [However, resistance is bound to occur as the median duration of radiographic response is 5.6 months and 47 weeks, in patients treated with AA and MDV3100, respectively . Acquiree TMPRSS2. The facdeclines . Howeversibility . Newer tsibility . Other tsibility . If thesInvestigations are ongoing to develop more specific and sensitive tools to detect bone changes in prostate cancer. PET scans with different tracers have been studied with various success for its ability to detect metastatic diseases, monitor response to therapies and prognosticate OS . DigitalCirculating tumor cell (CTC) count has also been widely implemented in various clinical trials and can be used for risk-stratification, molecular subclassification, or as a surrogate endpoint in treatment efficacy studies. The decline of CTC count after various treatments has been associated with improved OS ,50. The Several new treatment options have recently become available for patients with mCRPC. Clinicians are now faced with the challenge of understanding how to best utilize these newer therapies. The post-docetaxel era has seen numerous trials combining docetaxel with multiple agents with distinct mechanisms of action including TKIs, angiogenic inhibitors, bone-targeted agents, BCL-2 inhibitors, chemotherapies, immunologic agents, and vitamin D analogs . AnalysiHormonal therapy combined with docetaxel was also tested in a phase I trial using ketoconazole and docetaxel. Although docetaxel was given weekly , active tumor response was observed in 62% of patients with PSA response, and 28% with partial response in measurable disease . This trIn order to achieve sustained success in drug development, researchers must remain conscious of the challenges and limitations in conducting clinical trials in prostate cancer. Given the heterogeneity of the disease at the molecular level, it remains a challenge to identify suitable druggable target(s). Subsequent molecular studies are warranted to justify and/or validate the targeted therapy under investigation. Failures from several recent phase III trials based on expedited approaches in advancing a drug from phase I/II to III despite weak early phase trial data have taught us to be more selective about what agents to bring forward to be tested in the phase III setting. Reducing drug failures early in development is far more important than filling a pipeline with poorly chosen late-stage drugs.Biomarkers can revolutionize both the development and use of targeted therapeutics, but is contingent upon the establishment of a concrete validation process. During the qualification process, a biomarker should be tested in phase I and II efficacy trials to measure its robustness and validate its association with predicted clinical outcome. The incorporation of mechanism-based biomarker endpoints into early clinical trials has facilitated in making early “go-no go” decisions in drug development ,63 and rMetastatic castration resistant prostate cancer: Progressive metastatic prostate cancer despite castrate level of testosterone.Surrogate endpoints: Outcome measures that are intended to substitute for a clinical endpoint and are expected to predict clinical benefit based on scientific evidence.Promiscuous androgen receptor: Androgen receptor protein that acquired mutations leading to the activation of the androgen-signaling axis with ligands other than testosterone and dihydrotestosterone.Circulating tumor cell count: Enumeration of subpopulation of tumor cells derived from the primary cancer site which has been shown to correlate with survival in metastatic prostate cancer.Prostate cancer clinical trials working group: A group of expert clinical investigators who meet periodically in an effort to standardize the eligibility and outcome measures in clinical trials in patients with metastatic castration resistant prostate cancer.mCRPC, metastatic castration-resistant prostate cancer; AA, abiraterone acetate; AR, androgen receptor; TKI, tyrosine kinase inhibitor; OS, overall survival; PFS, progression-free survival; PSA, prostate-specific antigen; PCWG, prostate cancer clinical trials working group; ERG, ETS-related gene; CTC, circulating tumor cell.The authors indicated no potential conflicts of interests.All authors participated in concept design, data collection and analysis, drafting and critically revising the manuscript. All authors read and approve the final manuscript.Dr. William D. Figg is an internationally recognized pharmacologist and principle investigator of multiple prostate cancer clinical trials at the National Cancer Institute. He and his colleagues have made many original contributions in the advancement of prostate cancer therapeutics.


Reducing childhood mortality in resource-poor regions depends on effective interventions to decrease neonatal mortality from severe infection, which contributes up to a half of all neonatal deaths. There are key differences in resource-poor, compared to resource-rich, countries in terms of diagnosis, supportive care and treatment. In resource-poor settings, diagnosis is based on identifying clinical syndromes from international guidelines; microbiological investigations are restricted to a few research facilities. Low levels of staffing and equipment limit the provision of basic supportive care, and most facilities cannot provide respiratory support. Empiric antibiotic treatment guidelines are based on few aetiological and antimicrobial susceptibility data. Research on improving health care systems to provide effective supportive care, and implementation of simple pragmatic interventions, such as low-cost respiratory support, are essential, together with improved surveillance to monitor emerging drug resistance and treatment failures. Reductions in mortality will also be achieved through prevention of infection; including emerging vaccination and anti-sepsis strategies. Globally, under-5 mortality has declined by 28%, from 90 deaths per 1000 live births in 1990, to 65 in 2008 Here we aim to provide an overview of some of the key differences in management of severe infection in resource-poor compared to resource-rich settings, and consider research directions to improve management and to prevent infection. We restrict this paper to severe bacterial infection since there are limited data on congenital infections such as cytomegalovirus and rubella in resource-poor settings, but these are important areas for future research.2The principle causes of neonatal mortality are infection, birth asphyxia and preterm birth. In resource-poor settings, infection likely contributes to up to a half of all neonatal deaths 3In resource-poor settings, most sick newborns are not assessed and managed by specialist paediatricians. Clinicians are usually dependent on recognition of patterns of clinical signs and symptoms for diagnosis, which is central to management  [There are limitations to the use of clinical signs and symptoms for diagnosis of severe infection. Absence of microbiological culture investigation limits individual management; physicians are unable to rationalise and direct antibiotic treatment, and confirm their clinical diagnoses and there are particular difficulties in confirming the diagnosis of neonatal meningitis, for which signs and symptoms are non-specific. Lumbar puncture is an important diagnostic tool for neonatal meningitis, and can provide useful information even without the availability of microbiological culture ococcus) , as well4Resource-poor settings are limited in their ability to provide basic supportive care  by inadequate staffing (for example 2 trained staff to 100 children is not uncommon), as well as availability of training and equipment. Routine newborn documentation can be inadequate for care. Although simple admission pro forma, such as newborn admission records, can help improve clinical assessment and record keeping Where neonatal care is limited, alternatives to conventional care may be appropriate and beneficial. Kangaroo mother care has been shown to reduce neonatal infection at 40–41 weeks gestational age  in stabilised low birth weight neonates, but more work is needed to establish its use in neonates requiring more conventional neonatal support A specific and important element of neonatal supportive care, lacking in resource-poor settings, is respiratory support. This is due to deficiencies in equipment, and a lack of training for health care staff. There are, however, methods of providing mild to moderate respiratory support through continuous positive airway pressure (CPAP) which are potentially more feasible and low-cost for use in resource-poor settings. In some cases this can provide an alternative to conventional ventilation 5Developing appropriate treatment guidelines and evaluating their efficacy is challenging in resource-poor settings. In particular this relates to the lack of microbiological investigation, which means data on aetiology of neonatal infection and antibiotic sensitivities are scarce. International guidelines from the World Health Organisation, (WHO) Pocketbook of hospital care for Children, in common with guidelines in resource-rich settings, recommend broad-spectrum parenteral antibiotics, usually a combination of penicillin and gentamicin, or a third generation cephalosporin, based on covering common neonatal pathogens.Escherichia coli and Streptococcus agalactiae . GBS has only recently been identified as a pathogen in EOS in resource-poor settings Listeria monocytogenes is very rarely identified in EOS in resource-poor settings E. coli) such as Klebsiella pneumoniae, are more common in resource-poor settings. In late onset sepsis (LOS (48 h–28 days)) a key difference is the high incidence of coagulase negative Staphylococci (CONS) in resource-rich settings. This usually occurs in preterm neonates, associated with indwelling devices, such as percutaneous long lines. In resource-poor settings it is unclear whether it is a contaminant, or a pathogen, and the indwelling devices it is associated with are much less commonly used. There are similarities in aetiology too, however, as in both settings LOS is commonly caused by gram negative bacteria, Staphylococcus aureus and Streptococcus pneumoniaeThere are important differences in aetiology of neonatal infection in resource-poor and resource-rich settings however. In resource-rich settings, the leading causes of early onset neonatal sepsis (EOS (0–48 h)) are Assessment of continued efficacy of treatment guidelines is essential. In common with resource-rich settings, neonates in resource-poor settings are at increasingly high risk of hospital acquired infection and drug-resistant pathogens Improving neonatal care in the community is also important because of difficulties accessing health services in some areas. A large cluster randomised trial (39 intervention and 47 control villages) of a package of home-based neonatal care in rural India, including community treatment of neonatal sepsis, decreased neonatal sepsis case fatality from 16.2 to 2.8% 6Research to improve diagnostic methods, pragmatic interventions for supportive care and surveillance of drug-resistance for treatment of neonatal infection in resource-poor settings are high priorities, as described. However, research to prevent severe infection is also important, as discussed below.E coliDesign and implementation of immunisation is a key element of prevention and could build on and strengthen existing maternal immunisation programmes  in resource-poor settings. Potential vaccine candidates for neonatal sepsis include Group B Streptococcus (GBS), for which a trivalent conjugate vaccine is in phase II clinical trials in pregnant women in South Africa Antisepsis is another strategy, however vaginal chlorhexidine was shown to be ineffective before delivery in reducing neonatal sepsis in a randomised controlled trial of 8011 women in South Africa 7Improving management of severe infection in infancy is an international priority. Key factors in improving care in resource-poor settings are improved aetiological diagnosis and effective provision of supportive care, including non-invasive respiratory support. Effective prevention strategies through new vaccines and anti-sepsis interventions are important research directions.None.


Arabidopsis thaliana. Even though several summarizing attempts have been made, a general picture of gene expression changes in susceptible virus-host interactions is lacking.At the moment, there are a number of publications describing gene expression profiling in virus-infected plants. Most of the data are limited to specific host-pathogen interactions involving a given virus and a model host plant – usually Arabidopsis-virus interactions. We used the mean r (Pearson’s correlation coefficient) for neighboring pairs to estimate pairwise local similarity in expression in the Arabidopsis genome.To analyze transcriptome response to virus infection, we have assembled currently available microarray data on changes in gene expression levels in compatible Here we provide a functional classification of genes with altered expression levels. We also demonstrate that responsive genes may be grouped or clustered based on their co-expression pattern and chromosomal location.Arabidopsis genome, thus underlining a role of the specific biological processes in common mechanisms of general resistance against viruses and in physiological/cellular changes caused by infection. Using integrative platforms for the analysis of gene expression data and functional profiling, we identified overrepresented functional groups among activated and repressed genes. Each virus-host interaction is unique in terms of the genes with altered expression levels and the number of shared genes affected by all viruses is very limited. At the same time, common genes can participate in virus-, fungi- and bacteria-host interaction. According to our data, non-homologous genes that are located in close proximity to each other on the chromosomes, and whose expression profiles are modified as a result of the viral infection, occupy 12% of the genome. Among them 5% form co-expressed and co-regulated clusters.In summary, we found that there is a greater variety of upregulated genes in the course of viral pathogenesis as compared to repressed genes. Distribution of the responsive genes in combined viral databases differed from that of the whole  R) genes that are abundant in every plant species [R genes to a specific viral pathogen, viruses induce a variety of responses to prime and elevate their infections. These include expression changes associated with cellular processes redirected by viruses for their demands and host defensive reactions to the pathogenesis [Viruses are among the most agriculturally important groups of plant pathogens, causing serious economic losses in many major crops by reducing yield and quality . Althoug species , they imogenesis . UnderstAt the moment, there are a number of publications describing gene expression profiling in virus-infected plants that are derived mostly from DNA microarrays. They indicate a significant impact of viral infection on a wide array of cellular processes . UsuallyArabidopsis thaliana. In spite of several efforts to summarize general changes in plant gene expression  having been made [Most of the data are limited to specific host-pathogen interactions involving a given virus and a model host plant, which usually is een made -5,11, a Arabidopsis-virus interactions and attempted to create a functional classification of the genes with altered expression levels. We conclude that each virus-host interaction is unique in terms of the genes with altered expression levels and the number of shared genes affected by all viruses is very limited. Importantly, we also demonstrate that responsive genes may be grouped or clustered based on their co-expression pattern and chromosomal location.In this work, in order to analyze transcriptome response to virus infection, we have assembled currently available microarray data on changes in gene expression levels in compatible Arabidopsis expression data were obtained from Nottingham Arabidopsis Stock Centre microarray (NASC), ArrayExpress from the European Bioinformatics Institute database and the Gene Expression Omnibus database. Additional data were retrieved from supplementary material of published papers [see Additional file P < 0.05. We selected only those genes that significantly changed their expression level in response to pathogen attack by at least two-fold. Tandem duplicates were removed from the resulting profile. The total number of collected genes across all experiments was 52488. These data represent 44 experiments with 3 different types of pathogens: virus, bacteria and fungus. Among them there were 11 viruses and the total number of genes with significantly altered expression elicited by these viruses was 16816. This number included many identical genes (with the same ID) recorded in different experiments. After subtraction of the repeating genes, a list of 7639 unique genes was obtained. The same data set was used to obtain data for bacteria 17734 (11409 unique genes) and 15426 for fungi (among them 11047 unique genes).Arabidopsis genes. To find over-represented functional groups among activated or repressed genes during virus-host interactions we used Babelomics 4 FatiGO [We performed a meta-analysis of all the collected data on compatible virus-host interactions and also on the whole database representing viral, bacterial and fungal interactions with the host plant. We used tools from TAIR to search GO annotations and functionally classify 4 FatiGO  and SAE 4 FatiGO . To visu4 FatiGO .r) of the expression level for these genes. To test for pairwise local similarity in expression in the Arabidopsis genome, the mean r of the expression profiles for neighboring pairs of genes was calculated [The level of co-expression between two genes was defined as the Pearson’s correlation coefficient , Cauliflower mosaic virus (CAMV), Cucumber mosaic virus (CMV), Lettuce mosaic virus (LMV), Plum pox virus (PPV), Turnip crinkle virus (TCV), Tobacco etch virus (TEV), Tobacco mosaic virus (TMV and TMV-Cg), Tobacco rattle virus (TRV), Turnip mosaic virus (TuMV) and Oilseed rape mosaic tobamovirus (ORMV) [To analyze plant response to virus infection, we have assembled currently available microarray data on changes of gene expression levels in s (ORMV) ,10,16-22Arabidopsis genome. These are the genes either needed for the host to defend itself against the virus or for the virus to re-arrange host cellular machinery for its own needs. More than two thirds of these genes (69%) were always upregulated and only 13% were always downregulated. A sizeable portion of the genes (17%) had differential expression in response to infection with different viruses . However, this number included many identical genes (with the same ID) recorded in different experiments. After subtraction of the repeated genes, a list of 7639 unique genes was obtained [see Additional file De facto, it depends on several conditions. First, individual databases available for different viruses differ extensively in the number of repressed or induced genes and combined analysis is greatly influenced by this ratio in the most comprehensive databases. Second, as mentioned above, the pool of upregulated genes is larger because of the greater variety of affected genes whereas the quantity of downregulated genes is limited. Otherwise stated, more diverse genes are upregulated during different virus infections whereas downregulated genes tend to be common regardless of the particular virus. Lastly, a more accurate illustration of the general status of gene expression changes can be derived from the analysis of their proportional representation in the sets of induced or repressed genes within each functional category, which is the subject of the following section.Does the larger number of activated genes as compared to repressed genes correspond to a general trend of plant response to virus, reflecting a greater diversity of upregulated genes? In other words, based on this information, can we conclude as other authors have done , that thUsing TAIR’s functional categorization, we first assigned each gene to one of the three main gene ontologies (GO) - Biological Process, Cellular Components and Molecular Function, and next to a specific functional category (FC). It is important to emphasize three key points when relying on the GO terms in analyzing expression profiles: their generality, their obvious redundancy and their incompleteness. Redundant annotations and multiple descriptions of the same biological mechanisms represent special concern undermining an effort to address consistency in characterization of gene products. Still, the Gene Ontology project  currentlFigure Arabidopsis with the corresponding distribution within our database of genes that are involved in response to virus infection , where ni and nj are the number of genes with altered expression level belonging to the database for virus i and virus j, respectively, and nij represents the number of genes shared between both viruses [Sij; the higher this value is, the more similarity that exists between the two compared virus-host interactions.To find common responses to different viruses, we compared patterns of gene response in individual susceptible interactions. In order to do this, we used the number of shared genes among every pair of viruses to compute a similarity matrix between them according to the formula  viruses . Next, wAs presented in Figure Although the number of common genes affected by all viruses is very limited, each virus-host interaction is unique in terms of which genes have altered expression levels. Among them are several pathogenesis-related (PR) genes, albeit they seem to be specifically upregulated in response to particular viruses: CalCuV, TMV and TEV (PR1), CMV, CalCuV, TMV and TRV (PR2 and PR4), LMV and TRV (PR5), CMV and TMV (PR3).Overall, we have found only 198 genes that frequently change their expression in response to the majority of the viruses [see Additional file To identify overrepresented functional groups among activated or repressed genes, we subjected genes to analysis by Babelomics 4 FatiGO  and SEA When implemented with the assembled data set, FatiGO and SEA identified over-represented FC and subcategories among the sets of induced or repressed genes belonging to each of the main GO domains. Overrepresented in the set of repressed genes were those involved in defense response, hormone signaling , response to external stimulus, photosynthesis and bioenergetics processes (encoding photosystem I and II proteins and electron transport chain) [see Additional file Overrepresented in the set of induced genes were those participating in response to abiotic stimulus, responses to organic and inorganic substances, nitrogen component metabolic processes and protein transport . The latter host pathways are essential for facilitating virus intracellular movement. Another example of a biological process that was found only in the upregulated gene set is chromatin organization (histone modification). Chromatin structural features and posttranslational modifications play a crucial role in the regulation of gene expression . EpigeneAssembling information from multiple sources, such as different microarray platforms, experimental conditions, stages of infection when samples were collected, etc. raises a question of the integrity of the combined data, since it is hardly possible to eliminate the “batch effect” from influencing final results. Even so, these disparities are not likely to change the biological truth. For instance, as presented in Figure Applying agriGO tools, we found that early, non-symptomatic, phases of infection are characterized by massive induction of genes belonging to both common and stress-responsive pathways. Overrepresented in the set of activated genes were amine biosynthetic processes, aromatic amino acid family metabolic processes, photosynthetic activity and responses to biotic and abiotic stresses Figure . Late stOne of the main features of the late host response is repression of photosynthetic and energy pathways: photosystem I and II assembly, pentose-phosphate cycle, etc. Figure . ChlorosArabidopsis genome may further be divided into co-regulated and co-expressed blocks of genes or clusters. Since microarray data sets on susceptible host-virus interactions were not large enough to statistically predict clusters of genes with similar expression changes, we combined them with data from microarray experiments representing bacterial-host and fungal-host interactions and then used “viral sets” as a base for filtering out only analogous genes. This way, we were able to compose groups of co-expressed genes.While looking at the data derived from the analysis of publicly available microarray repositories, we noticed that genes with expression profiles modified as a result of viral infection were often (12% of genome) located in close proximity to each other on the same chromosomes. Analyzing only close proximity and differential response to the infection (repressed or activated genes) we discovered 1594 such groups of genes  and possibly co-regulated but share no sequence homology. Although most of them were differentially expressed, 22 clusters were always upregulated and only 2 clusters were always downregulated. Among all identified clusters only two contained four genes, nine were composed of three genes, and eighty-six contained two genes  so that genes of different GO categories that are involved in defense mechanisms are engaged [Therefore, co-expressed neighbors do not seem to be associated with a particular GO . However engaged .Interestingly, one of the clusters includes three genes encoding leucine-rich repeat (LRR) family proteins: AT1G33590, AT1G33600 and AT1G33610. Two more genes that are absent in available microarray data sets, AT1G33612 and AT1G33670, also encode LRR proteins and are located in the same chromosomal region. In addition, we found three other clusters containing genes with common domain structure and functional characteristics: i. cluster with a Toll-Interleukin-Resistance (TIR) domain (AT1G72900 and AT1G72910); ii. cluster with genes encoding SAM superfamily proteins ; and iii. cluster with genes encoding histone superfamily proteins (AT4G40030 and AT4G40040).Arabidopsis thaliana[Previously, we reported on the clustering of pathogen-response genes in the genome of  thaliana. That st thaliana. While cArabidopsis genes responsive to viral infections using currently available microarray data. For comparison, we also put together genes derived from microarray experiments with bacteria and fungi. Since there is significantly more information on changes in plant gene expression due to infection with bacteria and fungi, we limited the number of genes to approximately the same number as was compiled for viruses: 17734 for bacteria (11409 unique genes) and 15426 for fungi (among them 11047 unique genes) [As mentioned above, we tried to assemble the largest possible database of e genes) -36. Gene expression changes in response to all pathogens were very similar. In spite of specific interactions between host plants and each of the pathogens, nearly half of the genes associated with viral infections in susceptible hosts were also involved in response to bacterial or fungal infections Figure . Next, wR gene-mediated resistance.While determining significantly over-represented functional groups that include genes activated during virus-host interactions, we have also found groups of genes whose biological functions are common for all three pathogens  regardless of whether there is a susceptible or resistant type of interaction. To obtain significantly over-represented GO terms from gene sets upregulated during infection with these pathogens, we used the SAE tool from agriGO . In ordeArabidopsis-virus interactions. In summary, we found that there is a greater variety of upregulated genes in the course of viral pathogenesis as compared to repressed genes. Distribution of the responsive genes in combined viral databases differed from that of the whole Arabidopsis genome, thus underlining a role of the specific FC in common mechanisms of general resistance against viruses and in physiological/cellular changes caused by infection. Using integrative platforms for the analysis of gene expression data and functional profiling, we identified overrepresented functional groups among activated and repressed genes, which provided an in-depth view of the role of certain biological processes in response to infection. Each virus-host interaction was found to be unique in terms of the genes with altered expression levels, and the number of common genes affected by all viruses was very limited. We discovered that genes with expression profiles modified as a result of viral infection were often located in close proximity to each other on the same chromosomes forming a multiple clusters, consisting of physically linked and functionally related genes. Finally, combining genes derived from microarray experiments with bacteria and fungi with a viral data set, we observed that gene expression changes in response to all pathogens were very similar and that nearly half of the genes associated with viral infections in susceptible hosts were also involved in response to bacterial or fungal infections.We have assembled currently available microarray data on changes in gene expression levels in compatible HR, Hypersensitive response; CalCuV, Cabbage leaf curl virus; CAMV, Cauliflower mosaic virus; CMV, Cucumber mosaic virus; LMV, Lettuce mosaic virus; PPV, Plum pox virus; TCV, Turnip crinkle virus; TEV, Tobacco etch virus; TMV and TMV-Cg, Tobacco mosaic virus; TRV, Tobacco rattle virus; TuMV, Turnip mosaic virus; ORMV, Oilseed rape mosaic tobamovirus; GO, Gene ontology annotations; ET, Ethylene; JA, Jasmonic acid; ABA, Abscisic acid.The authors declare that they have no competing interests.OP collected and analyzed the data. LN wrote the manuscript. All authors discussed the results and commented on the manuscript. All authors read and approved the final manuscript.Microarray Sources.Click here for fileA list of unique genes participating in response to virus infection.Click here for fileComparison of % coverage of different FC between whole genome and virus responsive genes in the assembled database.Click here for fileOver-represented GO in response to susceptible virus interactions.Click here for fileCommon genes in response to susceptible virus interactions.Click here for fileCluster genes.Click here for fileCommon genes in response to three pathogens.Click here for file


Our knowledge of the pathophysiology of affect dysregulation has progressively increased, but the pharmacological treatments remain inadequate. Here, we summarize the current literature on deficits in somatostatin, an inhibitory modulatory neuropeptide, in major depression and other neurological disorders that also include mood disturbances. We focus on direct evidence in the human postmortem brain, and review rodent genetic and pharmacological studies probing the role of the somatostatin system in relation to mood. We also briefly go over pharmacological developments targeting the somatostatin system in peripheral organs and discuss the challenges of targeting the brain somatostatin system. Finally, the fact that somatostatin deficits are frequently observed across neurological disorders suggests a selective cellular vulnerability of somatostatin-expressing neurons. Potential cell intrinsic factors mediating those changes are discussed, including nitric oxide induced oxidative stress, mitochondrial dysfunction, high inflammatory response, high demand for neurotrophic environment, and overall aging processes. Together, based on the co-localization of somatostatin with gamma-aminobutyric acid (GABA), its presence in dendritic-targeting GABA neuron subtypes, and its temporal-specific function, we discuss the possibility that deficits in somatostatin play a central role in cortical local inhibitory circuit deficits leading to abnormal corticolimbic network activity and clinical mood symptoms across neurological disorders. Table 1). This raises interesting questions, including first; whether the somatostatin deficits observed in neurological disorders represent common, distinct, or partly overlapping mechanisms of symptoms across disorders and, second, what may be the causes and biological mechanisms underlying the selective neuronal vulnerability of somatostatin-expressing neurons. In addition, we review somatostatin findings associated with affect regulation at the genetic, cellular, and pharmacological levels in animal studies. So far, these findings suggest that somatostatin deficits across different brain systems and diseases may play a central role in the affective symptom dimension rather than non-specific signals in neurological disorders . As somatostatin itself is not an ideal drug target, including for antidepressant effect, we suggest that further studies characterizing the intrinsic properties and biological vulnerabilities of somatostatin-expressing neurons, may identify novel targets with implications for understanding the function of local cell circuits and brain regions underlying affective symptoms across several neurological disorders.Mood disturbances are commonly observed in many neurological disorders. The chronic, recurrent and long duration of mood disturbances not only place an enormous emotional and financial burden on patients, but also on their families and society. Nearly 10% of all primary care office visits are depression-related , but onlPatients with major depressive disorder (MDD) show decreased somatostatin levels in the cerebrospinal fluid CSF; , and trasomatostatin gene expression in the dorsolateral prefrontal cortex (dlPFC), subgenual anterior cingulate cortex (sgACC), and amygdala . Other types of GABAergic cell markers, such as parvalbumin and cholecystokinin, are mostly not affected by MDD , negative symptoms  and cognitive symptoms. Somatostatin deficits in schizophrenia are demonstrated by a reduction of CSF somatostatin , decreashe dlPFC , and deche dlPFC , caudal he dlPFC . Changeshe dlPFC , number he dlPFC , somatosAlzheimer’s disease is a neurodegenerative disease with neuropsychiatric symptoms . DecreasTable 1). Taken together, the cumulative evidence demonstrates that somatostatin deficits are common neurochemical and molecular features in individuals with neurological disorders, regardless of their categorical diagnosis. While somatostatin studies of cell number and gene expression in human postmortem brains suggest a specific alteration of somatostatin-positive neurons across neurological disorders, it is possible that changes and dys-synchronization of additional components of local neuronal circuits contribute to a common symptom dimension, which we speculate includes low affect and mood dysregulation. Hence, this review is not comprehensive, but rather, highlights the recent findings in brain somatostatin signaling and the potential role of somatostatin deficits in affect dysregulation for integrating categorical models of mood symptoms into a dimensional model across neurological disorders.The evidence outlined in this review provides only a glimpse of the potential full range of somatostatin deficits across neurological disorders, as multiple other brain regions and disease categories await further characterization  knockout or disruption of exon IV-expressing Bdnf transcripts show decreased somatostatin gene expression  is through the activation of inhibitory G protein (Gi) and the following inhibition of adenylyl cyclase, leading to reduction of cAMP levels, activation of phosphotyrosine phosphatases, and modulation of mitogen-activated protein kinases and phospholipase C  in the human somatostatin gene [C/T polymorphism (rs4988514)] is associated with increased risk in Alzheimer’s disease progression and additive effect with the APOE epsilon4 allele neurons are a diverse group of inhibitory cells which co-release neuropeptides in order to support a fine-tuning of neuronal signaling and architecture. The local inhibitory circuits provide spatiotemporal control of information processing through at least 20 subtypes of cortical GABA neurons, which are based on their expression of different calcium binding proteins and neuropeptides, localization, targeting, and differential electrophysiological properties. Recent detailed reviews on GABA neuron subpopulations have been published . ApproxiRecent reports focusing on the patterns of cortical neuronal connectivity show that somatostatin-expressing interneurons mediate the firing of pyramidal neurons with a fine level of specificity among cortical layers. Integrating optogenetic and electrophysiology approaches, mouse somatostatin-expressing interneurons in layer 2/3 of the somatosensory cortex provide a tonic inhibition to the distal dendrites of excitatory pyramidal neurons by sharpening selectivity during periods of quiet wakefulness, which may contribute to synchronized firing in cortical networks and sensorimotor integration . InteresKO) mice show intact motor coordination and motor learning, but have a significant impairment in motor learning as demands of motor coordination are increased. Overall, a detailed analysis demonstrated that SstKO mice are healthy, fertile, and show no overt behavioral phenotypes, including anxiety-like behavior in the open-field and fear conditioning tests. Notably, SstKO mice display high basal plasma levels of corticosterone and growth hormone  Chimeric somatostatin/dopamine molecule  Chimeric-somatostatin vaccinations (1 selective), ACQ090 (Sst3 selective) and Sst4 selective β peptide agonists  Universal somatostatin : a somatmolecule : a somatmolecule . An examinations : a fusioagonists . Despite2 receptor agonist, but not after infusions of the other four receptor agonists; antidepressant-like effects in the forced swim test are observed following infusions of either Sst2 or Sst3 agonists (1), synergizes with imipramine in causing antidepressant-like effects in the tail suspension test and increases Bdnf mRNA expression in the mouse cerebral cortex  and its receptor neurotrophic tyrosine kinase receptor type 2 (TrkB) have been implicated in mood disorders . BDNF-Trpression . Progrespression  and highpression . Mild oxpression , potentipression . Compariignaling . In contignaling . Hence, somatostatin expression . Clarifying the role of somatostatin and its regulation of GABA inhibition in affect regulation could provide new strategies for predicting, delaying, and treating neurological diseases with mood disturbances. A number of questions remain. For example, are the prevalent somatostatin deficits seen in multiple diseases reflected in a common symptom dimension, such as low mood, across neurological diseases? What are the critical events that determine the vulnerability of somatostatin-expressing neurons? And what are the pathogenic mechanisms that mediate the observed disease-related molecular and cellular phenotypes? One possibility is that inflammation, oxidative stress, aging, and reduced neurotrophic support may all converge to affect somatostatin-expressing neurons. Targeting these pathways may exert neuro-protective effects on somatostatin-expressing neurons, as a potential therapeutic approach with implications for several neuropsychiatric disorders and neurodegenerative diseases.Here we have focused on somatostatin, a GABA marker, down-regulated in MDD, schizophrenia, bipolar disorder, and neurodegenerative diseases. Exploring cross-disease molecular (somatostatin) and cellular (somatostatin-expressing interneurons) pathological findings suggests a dimensional pathological phenotype that is specific to the somatostatin gene/cell biological entity rather than to categorical brain disorders. Based on these results we speculate that common risk factors affecting somatostatin and somatostatin-expressing neurons may impact information processing in the cortical local circuits (The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Hepatitis-C-virus- (HCV-) related end-stage cirrhosis is the primary indication for liver transplantation in many countries. Unfortunately, however, HCV is not eliminated by transplantation and graft reinfection is universal, resulting in fibrosis, cirrhosis, and finally graft decompensation. The use of poor quality organs, particularly from older donors, has a highly negative impact on the severity of recurrence and patient/graft survival. Although immunosuppressive regimens have a considerable impact on the outcome, the optimal regimen after liver transplantation for HCV-infected patients remains unclear. Disease progression monitoring with protocol biopsy and new noninvasive methods is essential for predicting patient/graft outcome and starting antiviral treatment with the appropriate timing. Antiviral treatment with pegylated interferon and ribavirin is currently considered the most promising regimen with a sustained viral response rate of around 30% to 35%, although the survival benefit of this regimen remains to be investigated. Living-donor liver transplantation is now widely accepted as an established treatment for HCV cirrhosis and the results are equivalent to those of deceased donor liver transplantation. End-stage liver disease caused by chronic hepatitis C virus (HCV) infection is the leading cause of liver transplantation in developed countries , 2, inclHCV reinfection of liver allografts is universal, occurring just after reperfusion followed by a rapid increase in HCV ribonucleic acid (RNA) levels within 4 postoperative months . DiagnosOverall, cirrhosis develops in approximately 25% of liver transplant recipients range 8%–44%) after 5 to 10 years and this percentage is likely to increase with an increase in the follow-up period , 8. Once%–44% aftP < 0.0001; http://www.unos.org/) [The development of decompensated cirrhosis due to recurrent hepatitis C is now the most frequent cause of graft failure, patient death, and the need for retransplantation in HCV-infected recipients , 10–13. os.org/) .The poor outcome of HCV-positive recipients has resulted in the divergence in transplant outcomes between HCV-positive recipients and HCV-negative recipients. Improvements in organ preservation, surgical techniques, and postoperative care have dramatically improved the survival of HCV-negative recipients over the last two decades, whereas this has not been the case in HCV-positive recipients for whom outcome has remained unchanged or even worsened over time –17. This background indicates the importance of identifying the factors related to severe recurrent hepatitis C and monitoring disease progression.In the transplant setting, many factors contribute to disease progression compared with nontransplant patients , includiThe impact of donor age on outcome has gained increased attention due to the increased use of liver grafts from older donors, which reflects the absolute shortage of available organs. Accumulating data indicates that grafts from older donors are at greater risk for severe histologic findings, disease progression, and impaired graft/patient survival compared with those from younger donors , 18–25. The use of extended criteria for the donors is especially important for HCV-positive recipients, although studies evaluating long-term outcomes in HCV-positive recipients are lacking. Several studies revealed that grafts from HCV-positive donors could be used as safely as those from HCV-negative donors for hepatitis C cirrhosis , 31–34. On the other hand, ischemic injury to the graft seems to have a serious impact on patient/graft survival and disease progression –39. An iAs for steatosis of graft, despite early studies associating graft steatosis with poor function , 43, theAdditionally, several experienced centers reported that LDLT could be performed as safely as deceased donor liver transplantation (DDLT) with an equivalent outcome for HCV-positive recipients , 46–50.Studies evaluating the association between the severity of HCV recurrence and HCV genotype are conflicting. Some studies suggest that genotype 1b is associated with a poorer outcome , 51–53, The coexistence of hepatocellular carcinoma is reported to have a negative impact on HCV-positive recipient survival , 70–76.http://www.hivtransplant.com/) [ Coinfection of the human immunodeficiency virus (HIV) in patients with HCV cirrhosis, once considered to be a contraindication for liver transplantation, has now gained wider acceptance for liver transplantation, with the introduction of highly active antiretroviral therapy that increases survival of HIV/HCV coinfected patients and makes end-stage HCV cirrhosis the leading cause of death . Studiesnt.com/) . Early high viral loads at 7 days , 4 month Postoperative infection with cytomegalovirus (CMV) is associated with more severe HCV disease, increased progression to cirrhosis, and a higher rate of graft failure compared to those without CMV infection , 89–92.Metabolic syndrome occurs in half of HCV-infected recipients within the first 12 months after transplantation and is associated with a greater progression of fibrosis . SeveralIt is generally accepted that over-immunosuppression, such as steroid bolus and OKT3 as rejection therapy, and maintenance immunosuppression with triple-quadruple therapies at full dose are risk factors for HCV liver injury and are associated with a poorer outcome. The optimal immunosuppressive regimen for HCV-infected patients after liver transplantation remains unclear, however, despite several advances in our knowledge regarding the impact of various medications on HCV recurrence in parallel with the development of promising new drugs.Numerous early studies clearly demonstrated that steroid boluses and/or OKT3 administered for graft rejection in HCV-positive patients accelerate recurrent hepatitis C , 100–103Based on early perceptions that a steroid bolus for acute rejection accelerates hepatitis C progression, steroids were believed to increase HCV injury. Considering liver injury and the long-term side effects of steroids, steroids were routinely discontinued by 3 months in most liver transplant programs until 2002 . AnotherIn addition to early reports , 76, two Several studies, including a meta-analysis, have demonstrated that steroid-free protocols are not significantly different from other protocols with regard to viremia, patient survival, or fibrosis progression –114. ManIn vitro series revealed that cyclosporine inhibits HCV replication in a cell-based replicon model –119. SevBecause induction with OKT3 and alemtuzumab is strongly associated with severe recurrent HCV , 132, seAzathioprine and MMF are other immunosuppression maintenance drugs associated with disease progression in HCV-infected recipients. An early prospective study showed no effect of MMF in HCV-infected recipients . RecentlAlthough mTOR inhibitors have gained widespread use in selected transplant programs as maintenance agents because of their renal-sparing properties, few studies have evaluated the effect of those drugs on the course of recurrent hepatitis C –150. WhiThe risk of progression to cirrhosis can be predicted by the biochemical and histologic recurrence pattern. Aminotransferase peak, bilirubin level, and the presence of biochemical cholestasis are associated with a higher rate of progression to graft cirrhosis –153. His In this background, posttransplant monitoring with reliable methods is crucial for predicting patient/graft outcome, to make an early diagnosis of disease progression, and to start antiviral treatment at the appropriate time. There are two types of prevalent diagnostic methods for monitoring recurrent hepatitis C after liver transplantation; invasive (liver biopsy and measurement of hepatic venous pressure gradient) and noninvasive .Liver biopsy remains the gold standard and the key diagnostic criterion with which other tests are compared in assessing fibrosis. As discussed above, early studies demonstrated the prognostic value of liver biopsy at the time of recurrence and for monitoring disease progression within the first 12 months. With respect to antiviral treatment, a biopsy is essential not only to assess the severity of hepatitis but also to rule out rejection, and initiating treatment in earlier stages of fibrosis results in improved sustained viral response (SVR) rates –28. ConsThe estimation of liver stiffness  with transient elastography (Fibroscan) has been aggressively investigated and is reported to correlate well with the fibrosis progression of HCV-infected grafts after liver transplantation –166. TheOther noninvasive methods utilizing biochemical markers and predictive mathematical models of fibrosis have also been investigated , 169–175Strategies to improve the outcomes of liver transplantation in HCV-infected recipients include eradication of the HCV virus before transplantation with the use of pretransplant antiviral treatment, eradication of HCV virus early after transplantation preemptively to prevent graft damage, and treatment for established recurrent hepatitis C in the acute, or more commonly, chronic phase. Regardless of the antiviral treatment timing, interferon (INF), especially pegylated-INF (PEG-INF), in conjunction with ribavirin (RBV) are currently accepted as a standard key drugs according to the perspectives obtained in nontransplant populations. Antiviral treatment before transplantation is aimed at suppressing HCV viremia in liver transplant candidates, which may reduce or eliminate the risk of recurrent infection and disease progression, but this approach is severely limited by poor liver function, a high prevalence of nonresponders, severe cytopenia, and complications, including life-threatening infections . To dateViral kinetic studies demonstrated that viremia is minimal in the anheptic phase and immediately after surgery, but the viral load increases as early as the second posttransplant week, reaching its maximal level between the first and third posttransplant month, with even higher levels than those observed at pretransplant period . TherefoThe most widely accepted and used strategy is initiating antiviral therapy once recurrent hepatitis C in the graft is established by liver biopsies. Initial studies of monotherapy with IFN-alpha yielded poor results, with SVR rates lower than 5% . With thThe recent reports of PEG-INF/RBV treatment are summarized in Factors affecting SVR rates after PEG-INF/RBV therapy have been aggressively investigated in these studies. Non-1 genotype , 235, abIn the absence of controlled studies comparing different treatment regimens, it is not currently possible to determine whether to begin treatment with full or reduced doses and increase as tolerated, or whether individualized treatment is beneficial according to viral response kinetics. Therefore, the rules set out for the nontransplant population should be followed, but adherence to treatment is a major issue for posttransplant recipients. Dose reductions of RBV and/or PEG-INF are necessary in approximately 70% of patients and treatment discontinuation in approximately 30% . Dose-de An increased risk of acute rejection in patients treated with PEG-INF/RBV (5%-6%) compared with those with INF/RBV (1%–3%) was suggested by recent systematic reviews –197, altBased on the present perspectives, it is compelling to conclude that there is currently no evidence to support the recommendation of antiviral treatment for recurrent graft hepatitis C due to the lack of clinical benefit and frequent adverse effects, as concluded by the recent Cochrane meta-analysis . Recent In areas with low deceased donor organ availability like Japan, the indication of LDLT for HCV cirrhosis is similar to that of DDLT , whereasBased on accumulating reports comparing LDLT and DDLT for HCV cirrhosis, hepatitis C recurrence by itself does not seem to explain the differences in patient/graft survival between LDLT and DDLT, and even improved outcomes could be achieved in LDLT due to the better quality of the graft and less sick recipient condition at the time of transplantation. Thus, LDLT could be strongly recommended for HCV-positive patients whenever it is available.Graft reinfection by HCV is universal with a faster progression to fibrosis and cirrhosis compared with nontransplanted patients, and in those with decompensated graft cirrhosis, retransplantation is the only potentially curative option, although HCV infection has been identified as a risk factor in previous studies , 256–263Due to the lack of a clear consensus with a variety of reported factors, several models based on logistic regression analysis of donor and recipient factors have been developed in the decision-making process for elective retransplantation in HCV-infected patients. These models include the Rosen score , the MELHepatitis C is here to stay and will remain the most common indication for liver transplantation. Physicians treating HCV-infected candidates and recipients of liver transplantation must be aware of important issues that affect the natural history of recurrent HCV. At present, factors modifiable by clinicians include proper graft allocation, preservation injury, immunosuppression, and antiviral treatment, but many factors among these aspects remain to be determined in future well-designed prospective studies. LDLT can be performed as safely and effectively as DDLT for HCV-infected patients in experienced centers.


Oncolytic viruses (OVs) are novel immunotherapeutic agents whose anticancer effects come from both oncolysis and elicited antitumor immunity. OVs induce mostly immunogenic cancer cell death (ICD), including immunogenic apoptosis, necrosis/necroptosis, pyroptosis, and autophagic cell death, leading to exposure of calreticulin and heat-shock proteins to the cell surface, and/or released ATP, high-mobility group box 1, uric acid, and other damage-associated molecular patterns as well as pathogen-associated molecular patterns as danger signals, along with tumor-associated antigens, to activate dendritic cells and elicit adaptive antitumor immunity. Dying the right way may greatly potentiate adaptive antitumor immunity. The mode of cancer cell death may be modulated by individual OVs and cancer cells as they often encode and express genes that inhibit/promote apoptosis, necroptosis, or autophagic cell death. We can genetically engineer OVs with death-pathway-modulating genes and thus skew the infected cancer cells toward certain death pathways for the enhanced immunogenicity. Strategies combining with some standard therapeutic regimens may also change the immunological consequence of cancer cell death. In this review, we discuss recent advances in our understanding of danger signals, modes of cancer cell death induced by OVs, the induced danger signals and functions in eliciting subsequent antitumor immunity. We also discuss potential combination strategies to target cells into specific modes of ICD and enhance cancer immunogenicity, including blockade of immune checkpoints, in order to break immune tolerance, improve antitumor immunity, and thus the overall therapeutic efficacy. Oncolytic viruses (OVs) have been shown to be effective in treating cancer in preclinical models and promising clinical responses in human cancer patients –3. OV-meOncolytic viruses provide a number of potential advantages over conventional cancer therapies. First, OVs are tumor-selective antitumor agent, thus providing higher cancer specificity and better safety margin. Second, OV-mediated oncolysis not only leads to regression of tumor size, but this process provides key signals to dendritic cells (DCs) and other antigen presenting cells to initiate a potentially potent antitumor immune response. The immunogenic types of cell death induced by OVs provide danger signal  and a natural repertoire of tumor-associated antigens (TAAs) to DCs, both required to trigger an adaptive immunity against cancer –17. The In this review, we will discuss different modes of cell death induced by various OVs, their potential effects on the subsequent antitumor immunity. Then we discuss rationales and strategies of inducing ideal types of cancer cell death by either genetic modification on OVs or by combination with specific antitumor agents that lead to specific mode of immunogenic cancer cell death (ICD). Finally, we provide some perspective on future combination strategies to improve antitumor immunity for enhanced overall efficacy of virotherapy.Ideally, OVs selectively infect and replicate in cancer cells and cancer-associated endothelial cells, leading to direct oncolysis and subsequent antitumor activities without harming normal tissue –3. Some in trans expression of the non-structural late protein L4-100K increases both viral mRNA loading on ribosomes and late protein synthesis, accompanied by reduced phosphorylation of eIF2α and improved anticancer efficacy  does not infect normal murine cells, yet infect murine cancer cells even though the production of infectious virus progeny is often limited. A recent study may provide some answer to this phenomenon. McNeish et al. have found that murine cancer cells support viral gene transcription, mRNA processing, and genome replication of human Ad, but there is a profound failure of viral protein synthesis, especially late structural proteins with reduced loading of late mRNA onto ribosomes. Interestingly, efficacy . The keyin vivo are a critical danger signal for triggering antiviral immunity in the lung . These PRRs include the toll-like receptors (TLRs), retinoic acid-inducible gene-1 (RIG-1)-like receptors (RLRs), nucleotide oligodimerization domain (NOD)-like receptors (NLRs), AIM2-like receptors, and the receptor for advanced glycation end products (RAGE) , 27. It Matzinger proposed what is known now as the “danger theory” in 1994 . In the Damage-associated molecular patterns are molecules derived from normal cells that can initiate and perpetuate immunity in response to cell stress/tissue damage in the absence of pathogenic infection. DAMPs vary greatly depending on the type of cell and injured tissue. They can be proteins, DNA, RNA, or metabolic products. Protein DAMPs include intracellular proteins, such as high-mobility group box 1 (HMGB1), heat-shock proteins (HSPs), and proteins in the intracellular matrix that are generated following injury, such as hyaluronan fragments . HMGB1 iInvestigators have long been interested in what defines the immunogenicity of cancer cells and how we can enhance the immunogenicity for the purpose of immunotherapy. Pioneering work by Lindenmann and Klein almost half a century ago demonstrated that viral oncolysis of cancer cells by influenza virus increases immunogenicity of tumor cell antigens . HoweverOncolytic viruses kill cancer and associated endothelial cell through a variety of types of cell death as classically defined by the morphological and ultrastructural changes of dying cells. These include apoptosis, necrosis, necroptosis, pyroptosis, and autophagic cell death, often with one as the predominant form of death for a particular OV. By the new definition, cancer cell death induced by OVs is mostly immunogenic Table . ProbablCancer cell death induced by some OVs has not been examined for their direct features of ICD. However, other properties suggest that cancer cells infected by the OV are immunogenic, or the viruses themselves are highly immunogenic. Newcastle disease virus (NDV) is a well-studied virus for its virology and immunostimulatory properties . NDV ind+ T cells , an enzyme directly regulating RIP1 ubiquitination . Skin caThe fact that cancer cells resist certain death pathways will dictate to a degree which types of drugs (including OVs) to be used in therapeutic regimens. As we stated before, a number of OVs, such as VVs, often induces cancer cells into necroptotic cell death , 56, 57,We know now that immunogenic apoptosis, necrosis/necroptosis, and autophagic cell death are desired modes of cancer cell death because they are ICD. Is immunogenic apoptosis  better than other forms of ICD in the induction of antitumor immunity? We do not know for sure. This question needs to be addressed in the future. What we do know now is that there are strategies that can enhance the ICD and subsequent antitumor immunity. They can be classified into, genetic modification of OV vectors, combination with ICD inducers, and combination with specific immunostimulatory regimens.Cancer cells have usually accumulated a number of genetic mutations and epigenetic modifications that enable them to resist apoptosis. Based on this property, a number of OVs are built for high tumor selectivity by deleting viral genes encoding anti-apoptotic genes  promotes the cross-presentation of antigens from DCs to T cells. The autophagy could be induced by some OVs, or its inducer could be provided emselves , 128. Ho+ T cells. This significantly improved the therapeutic effectiveness of the oncolytic virus , chemokines (such as CCL5), or other innovative and artificial genes. We have recently reviewed the promising strategies of OVs in combination with other immunotherapeutic regimens . As we mic virus . Similaric virus . We haveic virus . Recentlic virus . This viic virus , 133.The tumor-associated immune tolerance is a big obstacle in cancer immunotherapy. Some armed OVs (such as a GM-CSF-armed oncolytic Ad) can break immune tolerance and generated antitumor immunity in at least some human cancer patients . In otheThe TME in the advanced stage of disease is highly immunosuppressive . This imIn order to improve the potency of antitumor immunity, one key step is the initial presentation of danger signal  and cross-presentation of TAAs . Recent studies demonstrated that ICD of cancer cells leads to potent danger signals, and autophagy in antigen donor cells, in this case cancer cells and associated endothelial cells, enhance the cross-presentation of TAAs to naïve T cells by DCs. Genetic engineering and combination strategies can skew the cancer cell death into modes of ICD and autophagy, leading to potent and sustained antitumor immunity and thus enhancing the efficacy of oncolytic immunotherapy. Which mode of ICD in the context of OVs is the most potent way to elicit antitumor immunity needs careful investigation in the near future. It is also important to keep in mind that oncolytic viruses modulate cancer immunogenicity through multiple mechanisms . Other tZong Sheng Guo collected and read relevant papers; designed and drafted the manuscript. David L. Bartlett and Zuqiang Liu have made suggestions to the manuscript. All authors have read and approved the final manuscript.David L. Bartlett is a scientific advisor for and has financial interest with Jennerex Biotherapeutics, a biopharmaceutical company developing oncolytic virotherapy. The other authors declare no conflict of interest.


Alcoholism is a chronic relapsing disorder characterized by continued alcohol use despite numerous adverse consequences. Alcohol has been shown to interact with numerous neurotransmitter systems to exert its pharmacological effects. The endogenous opioid system (EOS) has been strongly implicated in the positive and negative reinforcing effects of alcohol. Traditionally recognized as dysphoric/anhedonic in nature, the dynorphin/kappa-opioid receptor (DYN/KOR) system has recently received considerable attention due to evidence suggesting that an upregulated DYN/KOR system may be a critical contributor to the complex factors that result in escalated alcohol consumption once dependent. The present review will discuss alcohol-induced plasticity in the DYN/KOR system and how these neuroadaptations could contribute to excessive alcohol seeking and consumption. Alcohol use disorders, comprising alcohol abuse and dependence, pose a substantial physical, mental, and fiscal health risk to millions of people each year in the US, causing an average of 79,000 deaths and costing $224 billion annually , enkephalin (ENK), and dynorphin (DYN)  to the nucleus accumbens (Acb) or prefrontal cortex (PFC)] and extended amygdala  represent neurocircuitry related to motivational and cognitive decision making, as well as emotional, neurocircuitry thought to participate in the reinforcing effects of alcohol. Figure Understanding the acute neurobiological effects of alcohol is critically important because once known, it may be possible to predict the neuroadaptive, and resulting, behavioral impact of long-term alcohol exposure using theories such as the opponent-process theory of motivation  and produces excitatory or inhibitory post-synaptic potentials, respectively. D1-like receptor activation increases adenylyl cyclase activity by coupling to stimulatory G proteins (Gαs). This leads to an increase in the concentration of cyclic AMP (cAMP) and potentiation of cAMP-dependent protein kinases A (PKA) activity that further phosphorylates downstream signaling substrates. One signaling substrate is the transcription factor cAMP response element-binding protein (CREB) that activates the transcription of PDYN, BDNF, CRF, NPY, and other genes , it binds to its receptors  are not completely conserved across species. To address the ΔFosB hypothesis in the context of substance dependence in humans, FosB proteins in human brain were characterized by analysis of postmortem specimens, and compared their levels in the OFC and dlPFC, respectively between human controls and alcoholics  that destroys this site represents the allele that is associated with alcohol dependence. Thus, a SNP in the promoter of PDYN is associated with alcohol-dependence and may impact PDYN transcription in human brain. The impact of genetic variations on PDYN transcription may be relevant for diverse adaptive responses of this gene to alcohol.AP-1 may potentially regulate transcription of human prodynorphin gene in the human brain. Analysis of AP-1 constituents in the human brain demonstrated that canonical and noncanonical prodynorphin AP-1-binding element may be targeted by c-Jun and FosB proteins that form the dominant AP-1 complex  are associated with addiction, and (2) that overlap with CpG sites thus representing methylation-associated SNPs, or mSNPs Figure  Taqi et. The twoPDYN regulation in the brains of deceased human alcoholics  and intermediate  levels could contribute to altered distal events  in alcohol dependence. Therefore, increased DYN/KOR activity may induce a negative affective state in withdrawal and provide a basis for the negative reinforcing effects of alcohol. DYN/KORs in the Acb, Amyg and PFC/OFC may mediate the effects of chronic alcohol exposure in a brain region specific manner to decrease positive hedonic states, increase negative affective states or impair decision making and cognitive control, respectively. In addition, epigenetic mechanisms may also be involved in the upregulation of the DYN/KOR system following chronic alcohol exposure. Recent data supporting the role of the DYN/KOR system in mediating negative affective states also help to explain significant co-morbidity between alcohol use disorders and affective disorders. Taken together, the DYN/KOR system is heavily dysregulated in alcohol dependence and represents a potential therapeutic target to combat alcoholism.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Drosophila melanogaster has provided important new insight into the regulation of regenerative activity, innate immune homeostasis, commensal control, as well as age-related dysfunction in the intestine. Interestingly, many of the identified processes and mechanisms mirror similar homeostatic processes in the vertebrate intestine. This review summarized the current understanding of how innate immune responses, changes in commensal bacteria, and other challenges influence regenerative activity in the aging intestinal epithelium of flies and draws parallels to similar processes in mammals.As a barrier epithelium, the intestinal epithelium has to coordinate physiological functions like digestion and nutrient resorption with the control of commensal bacteria and the prevention of pathogenic infections. It can therefore mount powerful innate immune and inflammatory responses, while, at the same time, maintaining tissue homeostasis through regenerative processes. How these different functions are coordinated remains unclear, and further insight is required to understand the age-related loss of homeostasis in this system, as well as the etiology of inflammatory and proliferative diseases of the gut. Recent work in  As a major barrier epithelium, the intestinal epithelium is the first line of defense against pathogenic microorganisms, while at the same time managing the beneficial interaction between commensal bacteria and the host. Accordingly, it mounts highly coordinated and regulated stress and immune responses to govern these interactions. Dysfunction in these signaling mechanisms can cause intestinal dysbiosis and chronic inflammation, and these pathologies can in turn negatively influence epithelial homeostasis, causing dysplasias and cancers  form the majority of the midgut cell population, followed by hormone secreting enteroendocrine (EE) cells and the proliferating ISCs. ECs are absorptive cells but also secrete digestive enzymes in some parts of the gut, and play a central role in mounting innate immune responses to infection and in managing the commensal population. Proteases, lipases (such as LipA), carbohydratases, catalytic peptidoglycan recognition proteins (PGRPs) and lysozymes are among the digestive enzymes secreted by midgut cells  , and p38MAPK signaling pathways are essential for ISC proliferation  in both ECs and ISCs. Its activation in ISCs induces their proliferation by phosphorylating the AP-1 transcription factor Fos  by ECs in the intestinal epithelium , a member of the NADPH oxidase family, which is transcriptionally induced in ECs and activated in response to a bacterial challenge (Ha et al., Drosophila intestine contains a relatively simple microbiota comprising about 5–20 microbial species. Major constituents of these commensals are beneficial microbes, such as Acetobacter pomorum and Lactobacillus plantarum which promote growth and development in flies when reared on a restricted diet (Ryu et al., Gluconobacter morbifer, constitutes only a minor proportion of the healthy intestinal community. Under favorable conditions, however, it can take over the gut, causing gut pathologies and lethality of the host (Ryu et al., A young and healthy Drosophila immune system differentiates between friends and foes. Recent elegant work by the Lee lab shows, however, that pathogenic bacteria, in contrast to beneficial symbionts, are constantly secreting Uracil, which is recognized by the Drosophila immune system. Uracil is recognized by an unknown GPCR, which activates the PLCb/IP3/Ca/Duox pathway discussed above to produce ROS. Many opportunistic pathogens such as Vibrio fluvialis, Klebsiella pneumonia, Erwinia carotovora carotovora, Shigella sonnei, Pseudomonas aeruginosa and Serratia marcescens, but not symbionts like A. pomorum, L. plantarum and Commensalibacter intestini, secrete significant quantities of Uracil (Lee et al., G. morbifer leads to chronic inflammation, induces apoptosis and shortens Drosophila lifespan, while these effects were not observed in germ free control flies or in flies mono-associated with a mutant G. morbifer lacking Uracil secretion. Uracil-producing pathobionts may also contribute significantly to the age-related increase in epithelial Duox-mediated ROS production, and thus to the age-associated dysfunction in epithelial homeostasis. It is clear that understanding causes and consequences of age-related changes in the commensal microbiome is an important task for future studies.Until recently, it was not known how the Drosophila (Biteau et al., The Duox-induced innate immune response has thus important implications for the etiology of the dysfunction of the intestinal epithelium observed in aging flies. When flies are raised on a conventional diet, internal and external microbial populations expand with age (Ren et al., in vivo (Karpac et al., Why does the commensal microbiota expand in aging animals? It is unclear whether malfunctioning of the host immune response causes commensal populations to overgrow, or if expansion of immune-resistant intestinal commensals is the initiating event that causes the described aged-related intestinal pathology. Deregulation of innate immune signaling in aging epithelia can be observed, and may be brought about by age-related activation of stress signaling, in particular of the JNK signaling pathway (Buchon et al., Drosophila lifespan (Moskalev and Shaposhnikov, While germ-free conditions can rescue age-related dysplasia (Buchon et al., To maintain intestinal homeostasis, a highly selective immune response has to ensure that pathogenic microorganisms are eliminated, while commensals can thrive. Moreover, the inflammatory response triggered by pathogens and commensals alike has to be carefully contained to prevent excessive stem cell activation and dysplasias. It may not be surprising that these carefully balanced responses are misregulated in aging animals, making the host more susceptible to invading microbes, and promoting inflammatory and dysplastic conditions. A better understanding of the molecular parameters driving these age-related changes, however, promises to provide insight into avenues for therapeutic intervention that may not only be applied to inflammatory diseases and cancers of the gut, but potentially to allay tissue dysfunction in the normally aging human intestine.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.