Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria

Diagnosis of cerebral malaria: Tools to reduce Plasmodium falciparum associated mortality

Cerebral malaria (CM) is a major cause of mortality in Plasmodium falciparum (Pf) infection and is associated with the sequestration of parasitised erythrocytes in the microvasculature of the host's vital organs. Prompt diagnosis and treatment are key to a positive outcome in CM. However, current diagnostic tools remain inadequate to assess the degree of brain dysfunction associated with CM before the window for effective treatment closes. Several host and parasite factor-based biomarkers have been suggested as rapid diagnostic tools with potential for early CM diagnosis, however, no specific biomarker signature has been validated. Here, we provide an updated review on promising CM biomarker candidates and evaluate their applicability as point-of-care tools in malaria-endemic areas.

The Role of Hsp70s in the Development and Pathogenicity of Plasmodium falciparum

The main agent of human malaria, the protozoa, Plasmodium falciparum is known to infect liver cells, subsequently invading the host erythrocyte, leading to the manifestation of clinical outcomes of the disease. As part of its survival in the human host, P. falciparum employs several heat shock protein (Hsp) families whose primary purpose is to ensure cytoprotection through their molecular chaperone role. The parasite expresses six Hsp70s that localise to various subcellular organelles of the parasite, with one, PfHsp70-x, being exported to the infected human erythrocyte. The role of these Hsp70s in the survival and pathogenicity of malaria has received immense research attention. Several studies have reported on their structure-function features, network partnerships, and elucidation of their potential substrates. Apart from their role in cytoprotection and pathogenicity, Hsp70s are implicated in antimalarial drug resistance. As such, they are deemed potential antimalarial drug candidates, especially suited for co-targeting in combination therapies. In addition, Hsp70 is implicated in host immune modulation. The current report highlights the various structure-function features of these proteins, their roles in the development of malaria, current and prospective efforts being employed towards targeting them in malaria intervention efforts.

Mouse NC/Jic strain provides novel insights into host genetic factors for malaria research

Malaria is caused by Plasmodium parasites and is one of the most life-threatening infectious diseases in humans. Infection can result in severe complications such as cerebral malaria, acute lung injury/acute respiratory distress syndrome, and acute renal injury. These complications are mainly caused by P. falciparum infection and are major causes of death associated with malaria. There are a few species of rodent-infective malaria parasites, and mice infected with such parasites are now widely used for screening candidate drugs and vaccines and for studying host immune responses and pathogenesis associated with disease-related complications. We found that mice of the NC/Jic strain infected with rodent malarial parasites exhibit distinctive disease-related complications such as cerebral malaria and nephrotic syndrome, in addition to a rapid increase in parasitemia. Here, we focus on the analysis of host genetic factors that affect malarial pathogenesis and describe the characteristic features, utility, and future prospects for exploitation of the NC/Jic strain as a novel mouse model for malaria research.

Infection-Induced Resistance to Experimental Cerebral Malaria Is Dependent Upon Secreted Antibody-Mediated Inhibition of Pathogenic CD8+ T Cell Responses

Cerebral malaria (CM) is one of the most severe complications of Plasmodium falciparum infection. There is evidence that repeated parasite exposure promotes resistance against CM. However, the immunological basis of this infection-induced resistance remains poorly understood. Here, utilizing the Plasmodium berghei ANKA (PbA) model of experimental cerebral malaria (ECM), we show that three rounds of infection and drug-cure protects against the development of ECM during a subsequent fourth (4X) infection. Exposure-induced resistance was associated with specific suppression of CD8+ T cell activation and CTL-related pathways, which corresponded with the development of heterogeneous atypical B cell populations as well as the gradual infection-induced generation and maintenance of high levels of anti-parasite IgG. Mechanistically, transfer of high-titer anti-parasite IgG did not protect 1X infected mice against ECM and depletion of atypical and regulatory B cells during 4X infection failed to abrogate infection-induced resistance to ECM. However, IgMi mice that were unable to produce secreted antibody, or undergo class switching, during the repeated rounds of infection failed to develop resistance against ECM. The failure of infection-induced protection in IgMi mice was associated with impaired development of atypical B cell populations and the inability to suppress pathogenic CD8+ T cell responses. Our results, therefore, suggest the importance of anti-parasite antibody responses, gradually acquired, and maintained through repeated Plasmodium infections, for modulating the B cell compartment and eventually suppressing memory CD8+ T cell reactivation to establish infection-induced resistance to ECM.

Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions

Transcriptomics, the analysis of genome-wide RNA expression, is a common approach to investigate host and pathogen processes in infectious diseases. Technical and bioinformatic advances have permitted increasingly thorough analyses of the association of RNA expression with fundamental biology, immunity, pathogenesis, diagnosis, and prognosis. Transcriptomic approaches can now be used to realize a previously unattainable goal, the simultaneous study of RNA expression in host and pathogen, in order to better understand their interactions. This exciting prospect is not without challenges, especially as focus moves from interactions in vitro under tightly controlled conditions to tissue- and systems-level interactions in animal models and natural and experimental infections in humans. Here we review the contribution of transcriptomic studies to the understanding of malaria, a parasitic disease which has exerted a major influence on human evolution and continues to cause a huge global burden of disease. We consider malaria a paradigm for the transcriptomic assessment of systemic host-pathogen interactions in humans, because much of the direct host-pathogen interaction occurs within the blood, a readily sampled compartment of the body. We illustrate lessons learned from transcriptomic studies of malaria and how these lessons may guide studies of host-pathogen interactions in other infectious diseases. We propose that the potential of transcriptomic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in study design rather than as a consequence of technological constraints. Further advances will require the integration of transcriptomic data with analytical approaches from other scientific disciplines, including epidemiology and mathematical modeling.

Systems Biology-Based Investigation of Host-Plasmodium Interactions

Malaria is a serious, complex disease caused by parasites of the genus Plasmodium. Plasmodium parasites affect multiple tissues as they evade immune responses, replicate, sexually reproduce, and transmit between vertebrate and invertebrate hosts. The explosion of omics technologies has enabled large-scale collection of Plasmodium infection data, revealing systems-scale patterns, mechanisms of pathogenesis, and the ways that host and pathogen affect each other. Here, we provide an overview of recent efforts using systems biology approaches to study host-Plasmodium interactions and the biological themes that have emerged from these efforts. We discuss some of the challenges in using systems biology for this goal, key research efforts needed to address those issues, and promising future malaria applications of systems biology.

Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasite Eimeria falciformis to host immune defenses

Background

Parasites can either respond to differences in immune defenses that exist between individual hosts plastically or, alternatively, follow a genetically canalized (“hard wired”) program of infection. Assuming that large-scale functional plasticity would be discernible in the parasite transcriptome we have performed a dual RNA-seq study of the lifecycle of Eimeria falciformis using infected mice with different immune status as models for coccidian infections.

Results

We compared parasite and host transcriptomes (dual transcriptome) between naïve and challenge infected mice, as well as between immune competent and immune deficient ones. Mice with different immune competence show transcriptional differences as well as differences in parasite reproduction (oocyst shedding). Broad gene categories represented by differently abundant host genes indicate enrichments for immune reaction and tissue repair functions. More specifically, TGF-beta, EGF, TNF and IL-1 and IL-6 are examples of functional annotations represented differently depending on host immune status. Much in contrast, parasite transcriptomes were neither different between Coccidia isolated from immune competent and immune deficient mice, nor between those harvested from naïve and challenge infected mice. Instead, parasite transcriptomes have distinct profiles early and late in infection, characterized largely by biosynthesis or motility associated functional gene groups, respectively. Extracellular sporozoite and oocyst stages showed distinct transcriptional profiles and sporozoite transcriptomes were found enriched for species specific genes and likely pathogenicity factors.

Conclusion

We propose that the niche and host-specific parasite E. falciformis uses a genetically canalized program of infection. This program is likely fixed in an evolutionary process rather than employing phenotypic plasticity to interact with its host. This in turn might limit the potential of the parasite to adapt to new host species or niches, forcing it to coevolve with its host.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4095-6) contains supplementary material, which is available to authorized users.

Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

The shape of the experimental frequency distributions (EFD) of diverse molecular interaction events quantifying genome-wide binding is often skewed to the rare but abundant quantities. Such distributions are systematically deviated from standard power-law functions proposed by scale-free network models suggesting that more explanatory and predictive probabilistic model(s) are needed. Identification of the mechanism-based data-driven statistical distributions that provide an estimation and prediction of binding properties of transcription factors from genome-wide binding profiles is the goal of this analytical survey. Here, we review and develop an analytical framework for modeling, analysis, and prediction of transcription factor (TF) DNA binding properties detected at the genome scale. We introduce a mixture probabilistic model of binding avidity function that includes nonspecific and specific binding events. A method for decomposition of specific and nonspecific TF-DNA binding events is proposed. We show that the Kolmogorov-Waring (KW) probability function (PF), modeling the steady state TF binding-dissociation stochastic process, fits well with the EFD for diverse TF-DNA binding datasets. Furthermore, this distribution predicts total number of TF-DNA binding sites (BSs), estimating specificity and sensitivity as well as other basic statistical features of DNA-TF binding when the experimental datasets are noise-rich and essentially incomplete. The KW distribution fits equally well to TF-DNA binding activity for different TFs including ERE, CREB, STAT1, Nanog, and Oct4. Our analysis reveals that the KW distribution and its generalized form provides the family of power-law-like distributions given in terms of hypergeometric series functions, including standard and generalized Pareto and Waring distributions, providing flexible and common skewed forms of the transcription factor binding site (TFBS) avidity distribution function. We suggest that the skewed binding events may be due to a wide range of evolutionary processes of creating weak avidity TFBS associated with random mutations, while the rare high-avidity binding sites (i.e., high-avidity evolutionarily conserved canonical e-boxes) rarely occurred. These, however, may be positively selected in microevolution.

Immune activation and induction of memory: lessons learned from controlled human malaria infection with Plasmodium falciparum

Controlled human malaria infections (CHMIs) are a powerful tool to assess the efficacy of drugs and/or vaccine candidates, but also to study anti-malarial immune responses at well-defined time points after infection. In this review, we discuss the insights that CHMI trials have provided into early immune activation and regulation during acute infection, and the capacity to induce and maintain immunological memory. Importantly, these studies show that a single infection is sufficient to induce long-lasting parasite-specific T- and B-cell memory responses, and suggest that blood-stage induced regulatory responses can limit inflammation both in ongoing and potentially future infections. As future perspective of investigation in CHMIs, we discuss the role of innate cell subsets, the interplay between innate and adaptive immune activation and the potential modulation of these responses after natural pre-exposure.

Establishment of a murine model of cerebral malaria in KunMing mice infected with Plasmodium berghei ANKA

Malaria remains one of the most devastating diseases. Cerebral malaria (CM) is a severe complication of Plasmodium falciparum infection resulting in high mortality and morbidity worldwide. Analysis of precise mechanisms of CM in humans is difficult for ethical reasons and animal models of CM have been employed to study malaria pathogenesis. Here, we describe a new experimental cerebral malaria (ECM) model with Plasmodium berghei ANKA infection in KunMing (KM) mice. KM mice developed ECM after blood-stage or sporozoites infection, and the development of ECM in KM mice has a dose-dependent relationship with sporozoites inoculums. Histopathological findings revealed important features associated with ECM, including accumulation of mononuclear cells and red blood cells in brain microvascular, and brain parenchymal haemorrhages. Blood-brain barrier (BBB) examination showed that BBB disruption was present in infected KM mice when displaying clinical signs of CM. In vivo bioluminescent imaging experiment indicated that parasitized red blood cells accumulated in most vital organs including heart, lung, spleen, kidney, liver and brain. The levels of inflammatory cytokines interferon-gamma, tumour necrosis factor-alpha, interleukin (IL)-17, IL-12, IL-6 and IL-10 were all remarkably increased in KM mice infected with P. berghei ANKA. This study indicates that P. berghei ANKA infection in KM mice can be used as ECM model to extend further research on genetic, pharmacological and vaccine studies of CM.

Endothelial-Leukocyte Interaction in Severe Malaria: Beyond the Brain

Malaria is the most important parasitic disease worldwide, accounting for 1 million deaths each year. Severe malaria is a systemic illness characterized by dysfunction of brain tissue and of one or more peripheral organs as lungs and kidney. The most severe and most studied form of malaria is associated with cerebral complications due to capillary congestion and the adhesion of infected erythrocytes, platelets, and leukocytes to brain vasculature. Thus, leukocyte rolling and adhesion in the brain vascular bed during severe malaria is singular and distinct from other models of inflammation. The leukocyte/endothelium interaction and neutrophil accumulation are also observed in the lungs. However, lung interactions differ from brain interactions, likely due to differences in the blood-brain barrier and blood-air barrier tight junction composition of the brain and lung endothelium. Here, we review the importance of endothelial dysfunction and the mechanism of leukocyte/endothelium interaction during severe malaria. Furthermore, we hypothesize a possible use of adjunctive therapies to antimalarial drugs that target the interaction between the leukocytes and the endothelium.

Survival Rate and Transcriptional Response upon Infection with the Generalist Parasite Beauveria bassiana in a World-Wide Sample of Drosophila melanogaster

The ability to cope with infection by a parasite is one of the major challenges for any host species and is a major driver of evolution. Parasite pressure differs between habitats. It is thought to be higher in tropical regions compared to temporal ones. We infected Drosophila melanogaster from two tropical (Malaysia and Zimbabwe) and two temperate populations (the Netherlands and North Carolina) with the generalist entomopathogenic fungus Beauveria bassiana to examine if adaptation to local parasite pressures led to differences in resistance. Contrary to previous findings we observed increased survival in temperate populations. This, however, is not due to increased resistance to infection per se, but rather the consequence of a higher general vigor of the temperate populations. We also assessed transcriptional response to infection within these flies eight and 24 hours after infection. Only few genes were induced at the earlier time point, most of which are involved in detoxification. In contrast, we identified more than 4,000 genes that changed their expression state after 24 hours. This response was generally conserved over all populations with only few genes being uniquely regulated in the temperate populations. We furthermore found that the American population was transcriptionally highly diverged from all other populations concerning basal levels of gene expression. This was particularly true for stress and immune response genes, which might be the genetic basis for their elevated vigor.

Concurrent host-pathogen gene expression in the lungs of pigs challenged with Actinobacillus pleuropneumoniae

Background

Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcine host needs to be elucidated. However, research has traditionally focused on either bacteriology or immunology; an unbiased picture of the transcriptional responses can be obtained by investigating both organisms in the same biological sample.

Results

Host and pathogen responses in pigs experimentally infected with A. pleuropneumoniae were analyzed by high-throughput RT-qPCR. This approach allowed concurrent analysis of selected genes encoding proteins known or hypothesized to be important in the acute phase of this infection. The expression of 17 bacterial and 31 porcine genes was quantified in lung samples obtained within the first 48 hours of infection. This provided novel insight into the early time course of bacterial genes involved in synthesis of pathogen-associated molecular patterns (lipopolysaccharide, peptidoglycan, lipoprotein) and genes involved in pattern recognition (TLR4, CD14, MD2, LBP, MYD88) in response to A. pleuropneumoniae. Significant up-regulation of proinflammatory cytokines such as IL1B, IL6, and IL8 was observed, correlating with protein levels, infection status and histopathological findings. Host genes encoding proteins involved in iron metabolism, as well as bacterial genes encoding exotoxins, proteins involved in adhesion, and iron acquisition were found to be differentially expressed according to disease progression. By applying laser capture microdissection, porcine expression of selected genes could be confirmed in the immediate surroundings of the invading pathogen.

Conclusions

Microbial pathogenesis is the product of interactions between host and pathogen. Our results demonstrate the applicability of high-throughput RT-qPCR for the elucidation of dual-organism gene expression analysis during infection. We showed differential expression of 12 bacterial and 24 porcine genes during infection and significant correlation of porcine and bacterial gene expression. This is the first study investigating the concurrent transcriptional response of both bacteria and host at the site of infection during porcine respiratory infection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1557-6) contains supplementary material, which is available to authorized users.

Pathogenic CD8+ T cells in experimental cerebral malaria

Cerebral malaria (CM) is one the major complications occurring during malaria infection. The mechanisms leading to this syndrome are still not completely understood. Although it is clear that parasite sequestration is the key initiation factor, the downstream pathological processes are still highly debated. The experimental cerebral malaria (ECM) model, in which susceptible mice are infected with Plasmodium berghei ANKA, has led to the identification of CD8(+) T cells as the major mediator of ECM death. In this review, we discuss the recent advances and future developments in the understanding of the role of CD8(+) T cells in CM.

RNA-Seq-based analysis of changes in Borrelia burgdorferi gene expression linked to pathogenicity

Background

Lyme disease is a global public health problem caused by the spirochaete Borrelia burgdorferi. Our previous studies found differences in disease severity between B. burgdorferi B31- and B. garinii SZ-infected mice. We hypothesized that genes that are differentially expressed between Borrelia isolates encode bacterial factors that contribute to disease diversity.

Methods

The present study used high-throughput sequencing technology to characterize and compare the transcriptional profiles of B. burgdorferi B31 and B. garinii SZ cultured in vitro. Real-time quantitative RT-PCR was used to validate selected data from RNA-seq experiments.

Results

A total of 731 genes were differentially expressed between B. burgdorferi B31 and B. garinii SZ isolates, including those encoding lipoproteins and purine transport proteins. The fold difference in expression for B. garinii SZ versus B. burgdorferi B31 ranged from 22.07 to 1.01. Expression of the OspA, OspB and DbpB genes were significantly lower in B. garinii SZ compared to B. burgdorferi B31.

Conclusions

The results support the hypothesis that global changes in gene expression underlie differences in Borrelia pathogenicity. The findings also provide an empirical basis for studying the mechanism of action of specific genes as well as their potential usefulness for the diagnosis and management of Lyme disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-014-0623-2) contains supplementary material, which is available to authorized users.

Impact of 4-hydroxynonenal on matrix metalloproteinase-9 regulation in lipopolysaccharide-stimulated RAW 264.7 cells

Tissue degradation and leukocyte extravasation suggest proteolytic destruction of the extracellular matrix (ECM) during severe malaria. Matrix metalloproteinases (MMPs) play an established role in ECM turnover, and increased MMP-9 protein abundance is correlated with malarial infection. The malaria pigment hemozoin (Hz) is a heme detoxification biomineral that is produced during infection and associated with biologically active lipid peroxidation products such as 4-hydroxynonenal (HNE) adsorbed to its surface. Hz has innate immunomodulatory activity, and many of its effects can be reproduced by exogenously added HNE. Hz phagocytosis enhances MMP-9 expression in monocytes; thus, this study was designed to examine the ability of HNE to alter MMP-9 regulation in activated cells of macrophage lineage. Data show that treatment of lipopolysaccharide-stimulated RAW 264.7 cells with HNE increased MMP-9 secretion and activity. HNE treatment abolished the cognate tissue inhibitor of metalloproteinase-1 protein levels, further decreasing MMP-9 regulation. Phosphorylation of both p38 mitogen-activated protein kinase (MAPK) and c-Jun NH2-terminal kinase was induced by HNE, but only p38 MAPK inhibition lessened MMP-9 secretion. These results demonstrate the in vitro ability of HNE to cause MMP-9 dysregulation in an activated cell model. The findings may extend to myriad pathologies associated with lipid peroxidation and elevated MMP-9 levels leading to tissue damage.

Benzo pyrene-induced DNA adducts and gene expression profiles in target and non-target organs for carcinogenesis in mice

BACKGROUND

Gene expression changes induced by carcinogens may identify differences in molecular function between target and non-target organs. Target organs for benzo[a]pyrene (BaP) carcinogenicity in mice (lung, spleen and forestomach) and three non-target organs (liver, colon and glandular stomach) were investigated for DNA adducts by 32P-postlabelling, for gene expression changes by cDNA microarray and for miRNA expression changes by miRNA microarray after exposure of animals to BaP.

RESULTS

BaP-DNA adduct formation occurred in all six organs at levels that did not distinguish between target and non-target. cDNA microarray analysis showed a variety of genes modulated significantly by BaP in the six organs and the overall gene expression patterns were tissue specific. Gene ontology analysis also revealed that BaP-induced bioactivities were tissue specific; eight genes (Tubb5, Fos, Cdh1, Cyp1a1, Apc, Myc, Ctnnb1 and Cav) showed significant expression difference between three target and three non-target organs. Additionally, several gene expression changes, such as in Trp53 activation and Stat3 activity suggested some similarities in molecular mechanisms in two target organs (lung and spleen), which were not found in the other four organs. Changes in miRNA expression were generally tissue specific, involving, in total, 21/54 miRNAs significantly up- or down-regulated.

CONCLUSIONS

Altogether, these findings showed that DNA adduct levels and early gene expression changes did not fully distinguish target from non-target organs. However, mechanisms related to early changes in p53, Stat3 and Wnt/β-catenin pathways may play roles in defining BaP organotropism.

The quality of methods reporting in parasitology experiments

There is a growing concern both inside and outside the scientific community over the lack of reproducibility of experiments. The depth and detail of reported methods are critical to the reproducibility of findings, but also for making it possible to compare and integrate data from different studies. In this study, we evaluated in detail the methods reporting in a comprehensive set of trypanosomiasis experiments that should enable valid reproduction, integration and comparison of research findings. We evaluated a subset of other parasitic (Leishmania, Toxoplasma, Plasmodium, Trichuris and Schistosoma) and non-parasitic (Mycobacterium) experimental infections in order to compare the quality of method reporting more generally. A systematic review using PubMed (2000-2012) of all publications describing gene expression in cells and animals infected with Trypanosoma spp was undertaken based on PRISMA guidelines; 23 papers were identified and included. We defined a checklist of essential parameters that should be reported and have scored the number of those parameters that are reported for each publication. Bibliometric parameters (impact factor, citations and h-index) were used to look for association between Journal and Author status and the quality of method reporting. Trichuriasis experiments achieved the highest scores and included the only paper to score 100% in all criteria. The mean of scores achieved by Trypanosoma articles through the checklist was 65.5% (range 32-90%). Bibliometric parameters were not correlated with the quality of method reporting (Spearman's rank correlation coefficient <-0.5; p>0.05). Our results indicate that the quality of methods reporting in experimental parasitology is a cause for concern and it has not improved over time, despite there being evidence that most of the assessed parameters do influence the results. We propose that our set of parameters be used as guidelines to improve the quality of the reporting of experimental infection models as a pre-requisite for integrating and comparing sets of data.

Interferons and interferon regulatory factors in malaria

Malaria is one of the most serious infectious diseases in humans and responsible for approximately 500 million clinical cases and 500 thousand deaths annually. Acquired adaptive immune responses control parasite replication and infection-induced pathologies. Most infections are clinically silent which reflects on the ability of adaptive immune mechanisms to prevent the disease. However, a minority of these can become severe and life-threatening, manifesting a range of overlapping syndromes of complex origins which could be induced by uncontrolled immune responses. Major players of the innate and adaptive responses are interferons. Here, we review their roles and the signaling pathways involved in their production and protection against infection and induced immunopathologies.

Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system

In many systems, host-parasite evolutionary dynamics have led to the emergence and maintenance of diverse parasite and host genotypes within the same population. Genotypes vary in key attributes: Parasite genotypes vary in ability to infect, host genotypes vary in susceptibility, and infection outcome is frequently the result of both parties' genotypic identities. These host-parasite genotype-by-genotype (GH × GP) interactions influence evolutionary and ecological dynamics in important ways. Interactions can be produced through genetic variation; however, here, we assess the role of variable gene expression as an additional source of GH × GP interactions. The bumblebee Bombus terrestris and its trypanosome gut parasite Crithidia bombi are a model system for host-parasite matching. Full-transcriptome sequencing of the bumblebee host revealed that different parasite genotypes indeed induce fundamentally different host expression responses and host genotypes vary in their responses to the infecting parasite genotype. It appears that broadly and successfully infecting parasite genotypes lead to reduced host immune gene expression relative to unexposed bees but induce the expression of genes responsible for controlling gene expression. Contrastingly, a poorly infecting parasite genotype induced the expression of immunologically important genes, including antimicrobial peptides. A targeted expression assay confirmed the transcriptome results and also revealed strong host genotype effects. In all, the expression of a number of genes depends on the host genotype and the parasite genotype and the interaction between both host and parasite genotypes. These results suggest that alongside sequence variation in coding immunological genes, variation that controls immune gene expression can also produce patterns of host-parasite specificity.

Genes involved in host-parasite interactions can be revealed by their correlated expression

Molecular interactions between a parasite and its host are key to the ability of the parasite to enter the host and persist. Our understanding of the genes and proteins involved in these interactions is limited. To better understand these processes it would be advantageous to have a range of methods to predict pairs of genes involved in such interactions. Correlated gene expression profiles can be used to identify molecular interactions within a species. Here we have extended the concept to different species, showing that genes with correlated expression are more likely to encode proteins, which directly or indirectly participate in host–parasite interaction. We go on to examine our predictions of molecular interactions between the malaria parasite and both its mammalian host and insect vector. Our approach could be applied to study any interaction between species, for example, between a host and its parasites or pathogens, but also symbiotic and commensal pairings.

Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium

Malaria is a serious infectious disease that causes over one million deaths yearly. It is caused by a group of protozoan parasites in the genus Plasmodium. No effective vaccine is currently available and the elevated levels of resistance to drugs in use underscore the pressing need for novel antimalarial targets. In this review, we survey omics centered developments in Plasmodium biology, which have set the stage for a quantum leap in our understanding of the fundamental processes of the parasite life cycle and mechanisms of drug resistance and immune evasion.

A systems biological view of intracellular pathogens

As biomedical research becomes increasingly data-intensive, it is increasingly essential to integrate genomic-scale datasets, so as to generate a more holistic picture of complex biological processes. The systems biology paradigm may differ in strategy from traditional reductionist scientific methods, but the goal remains the same: to generate tenable hypotheses driving the experimental elucidation of biological mechanisms. Intracellular pathogens provide an excellent opportunity for systems analysis, as many of these organisms are amenable to genetic manipulation, allowing their biology to be played off against that of the host. Moreover, many of the most fundamental biological properties of these microbes (host cell invasion, immune evasion, intracellular replication, long-term persistence) are directly linked to pathogenesis and readily quantifiable using genomic-scale technologies. In this review, we summarize and discuss some of the available and foreseeable functional genomics datasets pertaining to host-pathogen interactions and suggest that the host-pathogen interface represents a promising, tractable challenge for systems biological analysis. Success will require developing and leveraging new technologies, expanding data acquisition, and increasing public access to comprehensive datasets, to assemble quantitative and testable models of the host-pathogen relationship.

P. falciparum modulates erythroblast cell gene expression in signaling and erythrocyte production pathways

Global, genomic responses of erythrocytes to infectious agents have been difficult to measure because these cells are e-nucleated. We have previously demonstrated that in vitro matured, nucleated erythroblast cells at the orthochromatic stage can be efficiently infected by the human malaria parasite Plasmodium falciparum. We now show that infection of orthochromatic cells induces change in 609 host genes. 592 of these transcripts are up-regulated and associated with metabolic and chaperone pathways unique to P. falciparum infection, as well as a wide range of signaling pathways that are also induced in related apicomplexan infections of mouse hepatocytes or human fibroblast cells. Our data additionally show that polychromatophilic cells, which precede the orthochromatic stage and are not infected when co-cultured with P. falciparum, up-regulate a small set of genes, at least two of which are associated with pathways of hematopoiesis and/or erythroid cell development. These data support the idea that P. falciparum affects erythropoiesis at multiple stages during erythroblast differentiation. Further P. falciparum may modulate gene expression in bystander erythroblasts and thus influence pathways of erythrocyte development. This study provides a benchmark of the host erythroblast cell response to infection by P. falciparum.

Comparative analysis of gene expression changes mediated by individual constituents of hemozoin

Plasmodium protozoa, the source of malarial infections, catabolize large quantities of hemoglobin during an intraerythrocytic phase. During this process, free heme is detoxified through biomineralization into an insoluble heme aggregate, hemozoin (Hz). In its native state, Hz is associated with a variety of lipid peroxidation products including 4-hydroxy-2-nonenal (HNE). In the present study, gene expression profiles were used to compare responses to two of the individual components of Hz in a model macrophage cell line. LPS-stimulated RAW 264.7 cells were exposed to HNE and the synthetic form of Hz, beta-hematin (BH), for 6 or 24 h. Microarray analysis identified alterations in gene expression induced by exposure to HNE and opsonized BH (fold change, > or = 1.8; p value, < or = 0.01). Patterns of gene expression were compared to changes induced by an opsonized control latex bead challenge in LPS-stimulated cells and revealed that the BH response was predominantly phagocytic. Ingenuity Pathway Analysis demonstrated that HNE mediated a short-term oxidative stress response and had a prolonged effect on the expression of genes associated with categories of "Cell Cycle", "Cellular Assembly and Organization", "DNA Replication, Recombination, and Repair", and "Cellular Development". Comparisons of expression changes caused by BH and HNE with those observed during malarial infection suggest that BH and HNE are involved in inflammatory response modulation, altered NF-kappaB signal transduction, extracellular matrix (ECM) degradation, and dyserythropoiesis. HNE exposure led to several significant steady-state expression changes including repressed chemokine (C-C motif) ligand 5 (Ccl5), indicative of dyserythropoiesis, and a severe matrix metalloproteinase 9 (Mmp9)/tissue inhibitor of metalloproteinase 1 (Timp1) imbalance in favor of ECM proteolysis.

Alterations in the Brain Transcriptome in Plasmodium Berghei ANKA Infected Mice

We have used cDNA microarrays to compare gene expression profiles in brains from normal mice to those infected with the ANKA strain of Plasmodium berghei, a model of cerebral malaria. For each of three brains in each group, we computed ratios of all quantifiable genes with a composite reference sample and then computed ratios of gene expression in infected brains compared to untreated controls. Of the almost 12,000 unigenes adequately quantified in all arrays, approximately 3% were significantly downregulated (P < 0.05, ≥ 50% fold change) and about 7% were upregulated. Upon inspection of the lists of regulated genes, we identified a high number encoding proteins of importance to normal brain function or associated with neuropathology, including genes that encode for synaptic proteins or genes involved in cerebellar function as well as genes important in certain neurological diseases such as Alzheimer's disease or autism. These results emphasize the important impact of malarial infection on gene expression in the brain and provide potential biomarkers that may provide novel therapeutic targets to ameliorate the neurological sequelae of this infection.

Small variant surface antigens and Plasmodium evasion of immunity

Antigenic variation at the Plasmodium-infected erythrocyte surface plays a critical role in malaria disease severity and host immune evasion. Our current understanding of the role of Plasmodium variant surface antigens in antigenic variation and immune evasion is largely limited to the extensive work carried out on the Plasmodium falciparum var gene family. Although homologues of var genes are not present in other malaria species, small variant gene families comprising the rif and stevor genes in P. falciparum and the pir genes in Plasmodium vivax, Plasmodium knowlesi and the rodent malaria Plasmodium chabaudi, Plasmodium berghei and Plasmodium yoelii also show features suggesting a role in antigenic variation and immune evasion. In this article, we highlight our current understanding of these variant antigens and provide insights on the mechanisms developed by malaria parasites to effectively avoid the host immune response and establish chronic infection.

Host-microbe interaction systems biology: lifecycle transcriptomics and comparative genomics

The use of microarray and comparative genomic technologies for the analysis of host-pathogen interactions has led to a greater understanding of the biological systems involved in infectious disease processes. Transcriptome analysis of intracellular pathogens at single or multiple time points during infection offers insight into the pathogen intracellular lifecycle. Host-pathogen transcriptome analysis in vivo, over time, enables characterization of both the pathogen and the host during the dynamic, multicellular host response. Comparative genomics using hybridization microarray-based comparative whole-genome resequencing or de novo whole-genome sequencing can identify the genetic factors responsible for pathogen evolutionary divergence, emergence, reemergence or the genetic basis for different pathogenic phenotypes. Together, microarray and comparative genomic technologies will continue to advance our understanding of pathogen evolution and assist in combating human infectious disease.

Oral activated charcoal prevents experimental cerebral malaria in mice and in a randomized controlled clinical trial in man did not interfere with the pharmacokinetics of parenteral artesunate

Background

Safe, cheap and effective adjunct therapies preventing the development of, or reducing the mortality from, severe malaria could have considerable and rapid public health impact. Oral activated charcoal (oAC) is a safe and well tolerated treatment for acute poisoning, more recently shown to have significant immunomodulatory effects in man. In preparation for possible efficacy trials in human malaria, we sought to determine whether oAC would i) reduce mortality due to experimental cerebral malaria (ECM) in mice, ii) modulate immune and inflammatory responses associated with ECM, and iii) affect the pharmacokinetics of parenteral artesunate in human volunteers.

Methods/Principal Findings

We found that oAC provided significant protection against P. berghei ANKA-induced ECM, increasing overall survival time compared to untreated mice (p<0.0001; hazard ratio 16.4; 95% CI 6.73 to 40.1). Protection from ECM by oAC was associated with reduced numbers of splenic TNF⁺ CD4⁺ T cells and multifunctional IFNγ⁺TNF⁺ CD4⁺ and CD8⁺ T cells. Furthermore, we identified a whole blood gene expression signature (68 genes) associated with protection from ECM. To evaluate whether oAC might affect current best available anti-malarial treatment, we conducted a randomized controlled open label trial in 52 human volunteers (ISRCTN NR. 64793756), administering artesunate (AS) in the presence or absence of oAC. We demonstrated that co-administration of oAC was safe and well-tolerated. In the 26 subjects further analyzed, we found no interference with the pharmacokinetics of parenteral AS or its pharmacologically active metabolite dihydroartemisinin.

Conclusions/Significance

oAC protects against ECM in mice, and does not interfere with the pharmacokinetics of parenteral artesunate. If future studies succeed in establishing the efficacy of oAC in human malaria, then the characteristics of being inexpensive, well-tolerated at high doses and requiring no sophisticated storage would make oAC a relevant candidate for adjunct therapy to reduce mortality from severe malaria, or for immediate treatment of suspected severe malaria in a rural setting.

Trial Registration

Controlled-Trials.com ISRCTN64793756

Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus

Relatively little is understood about the dynamics of global host-pathogen transcriptome changes that occur during bacterial infection of mucosal surfaces. To test the hypothesis that group A Streptococcus (GAS) infection of the oropharynx provokes a distinct host transcriptome response, we performed genome-wide transcriptome analysis using a nonhuman primate model of experimental pharyngitis. We also identified host and pathogen biological processes and individual host and pathogen gene pairs with correlated patterns of expression, suggesting interaction. For this study, 509 host genes and seven biological pathways were differentially expressed throughout the entire 32-day infection cycle. GAS infection produced an initial widespread significant decrease in expression of many host genes, including those involved in cytokine production, vesicle formation, metabolism, and signal transduction. This repression lasted until day 4, at which time a large increase in expression of host genes was observed, including those involved in protein translation, antigen presentation, and GTP-mediated signaling. The interactome analysis identified 73 host and pathogen gene pairs with correlated expression levels. We discovered significant correlations between transcripts of GAS genes involved in hyaluronic capsule production and host endocytic vesicle formation, GAS GTPases and host fibrinolytic genes, and GAS response to interaction with neutrophils. We also identified a strong signal, suggesting interaction between host gammadelta T cells and genes in the GAS mevalonic acid synthesis pathway responsible for production of isopentenyl-pyrophosphate, a short-chain phospholipid that stimulates these T cells. Taken together, our results are unique in providing a comprehensive understanding of the host-pathogen interactome during mucosal infection by a bacterial pathogen.

Role for parasite genetic diversity in differential host responses to Trypanosoma brucei infection

The postgenomic era has revolutionized approaches to defining host-pathogen interactions and the investigation of the influence of genetic variation in either protagonist upon infection outcome. We analyzed pathology induced by infection with two genetically distinct Trypanosoma brucei strains and found that pathogenesis is partly strain specific, involving distinct host mechanisms. Infections of BALB/c mice with one strain (927) resulted in more severe anemia and greater erythropoietin production compared to infections with the second strain (247), which, contrastingly, produced greater splenomegaly and reticulocytosis. Plasma interleukin-10 (IL-10) and gamma interferon levels were significantly higher in strain 927-infected mice, whereas IL-12 was higher in strain 247-infected mice. To define mechanisms underlying these differences, expression microarray analysis of host genes in the spleen at day 10 postinfection was undertaken. Rank product analysis (RPA) showed that 40% of the significantly differentially expressed genes were specific to infection with one or the other trypanosome strain. RPA and pathway analysis identified LXR/RXR signaling, IL-10 signaling, and alternative macrophage activation as the most significantly differentially activated host processes. These data suggest that innate immune response modulation is a key determinant in trypanosome infections, the pattern of which can vary, dependent upon the trypanosome strain. This strongly suggests that a parasite genetic component is responsible for causing disease in the host. Our understanding of trypanosome infections is largely based on studies involving single parasite strains, and our results suggest that an integrated host-parasite approach is required for future studies on trypanosome pathogenesis. Furthermore, it is necessary to incorporate parasite variation into both experimental systems and models of pathogenesis.

The pir multigene family of Plasmodium: antigenic variation and beyond

Multigene families are present on the telomeric and sub-telomeric regions of most chromosomes of the malaria parasite, Plasmodium. The largest gene family identified so far is the Plasmodium interspersed repeat (pir) multigene gene family and is shared by Plasmodium vivax, and simian and rodent malaria species. Most pir genes share a similar structure across the different species; a short first exon, long second exon and a third exon encoding a trans-membrane domain, and some pir genes can be assigned to specific sub-families. Although pir genes can be differentially transcribed in different life cycle stages, suggesting different functions, there is no clear link between sub-family and transcription pattern. Some of the pir genes encode proteins expressed on or near the surface of infected erythrocytes, and therefore could be potential targets of the host's immune response, and involved in antigenic variation and immune evasion. Other functions such as signalling, trafficking and adhesion have been also postulated. The presence of pir in rodent models will allow the investigation of this gene family in vivo and thus their potential as vaccines or in other interventions in human P. vivax infections.

Plasmodium chabaudi limits early Nippostrongylus brasiliensis-induced pulmonary immune activation and Th2 polarization in co-infected mice

Background

Larvae of several common species of parasitic nematodes obligately migrate through, and often damage, host lungs. The larvae induce strong pulmonary Type 2 immune responses, including T-helper (Th)2 cells as well as alternatively activated macrophages (AAMφ) and associated chitinase and Fizz/resistin family members (ChaFFs), which are thought to promote tissue repair processes. Given the prevalence of systemic or lung-resident Type 1-inducing pathogens in geographical areas in which nematodes are endemic, we wished to investigate the impact of concurrent Type 1 responses on the development of these Type 2 responses to nematode larval migration. We therefore infected BALB/c mice with the nematode Nippostrongylus brasiliensis, in the presence or absence of Plasmodium chabaudi chabaudi malaria parasites. Co-infected animals received both infections on the same day, and disease was assessed daily before immunological measurements were taken at 3, 5, 7 or 20 days post-infection.

Results

We observed that the nematodes themselves caused transient loss of body mass and red blood cell density, but co-infection then slightly ameliorated the severity of malarial anaemia. We also tracked the development of immune responses in the lung and thoracic lymph node. By the time of onset of the adaptive immune response around 7 days post-infection, malaria co-infection had reduced pulmonary expression of ChaFFs. Assessment of the T cell response demonstrated that the Th2 response to the nematode was also significantly impaired by malaria co-infection.

Conclusion

P. c. chabaudi co-infection altered both local and lymph node Type 2 immune activation due to migration of N. brasiliensis larvae. Given recent work from other laboratories showing that N. brasiliensis-induced ChaFFs correlate to the extent of long-term lung damage, our results raise the possibility that co-infection with malaria might alter pulmonary repair processes following nematode migration. Further experimentation in the co-infection model developed here will reveal the longer-term consequences of the presence of both malaria and helminths in the lung.

Relative avidity, specificity, and sensitivity of transcription factor-DNA binding in genome-scale experiments

One of the most crucial problems with genome-wide experimental analysis is how to extract meaningful biological phenomena from the resulting large data sets. Here, we present modeling and prediction techniques that are applied to genome-wide identification of in vivo protein-DNA binding sites from ChIP-based data sets. We develop a simple mixture probabilistic model of occurrence of non-specific and specific TF-DNA binding events for transcription factor binding to any site in the genome. We calculated the statistical significance of specific and non-specific random binding events using Kolmogorov-Waring and exponential functions, respectively. The binding events in the chromosome regions associated with non-specific, non-random binding loci were also identified and filtered out. The mixture model fits equally well to five different TFs (ERE, CREB, STAT1, Nanog, Oct4) data provided by ChIP-PET, SACO, and ChIP-Seq methods included in this study. We present a uniform methodology for estimating specificity, total number of binding sites, and sensitivity of data sets detected by these ChIP-based genome-wide experimental systems. We demonstrate strong heterogeneity of specific TF-DNA binding sites in terms of their avidity and by correlation between observed relative binding avidity of specific TF-DNA binding site and the level of mRNA transcription of the nearest gene target. Finally, we conclude that the sensitivity problem has not been resolved by current ChIP-based methods, including ChIP-Seq.

Differential gene expression mediated by 15-hydroxyeicosatetraenoic acid in LPS-stimulated RAW 264.7 cells

Background

Given the immuno-modulatory activity of native haemozoin (Hz), the effects of constitutive Hz components on immune response are of interest. Recently, gene expression changes mediated by HNE and the synthetic analogue of Hz, beta-haematin (BH), were identified and implicated a significant role for lipid peroxidation products in Hz's activity. The study presented herein examines gene expression changes in response to 15(S)-hydroxyeicosatetraenoic acid (HETE) in a model macrophage cell line.

Methods

LPS-stimulated RAW 264.7 macrophage-like cells were treated with 40 μM 15(S)-HETE for 24 h, and microarray analysis was used to identify global gene expression alterations. Fold changes were calculated relative to LPS-stimulated cells and those genes altered at least 1.8-fold (p value ≤ 0.025) were considered to be differentially expressed. Expression levels of a subset of genes were assessed by qRT-PCR and used to confirm the microarray results.

Results

Network analysis revealed that altered genes were primarily associated with "lipid metabolism" and "small molecule biochemistry". While several genes associated with PPAR-gamma receptor-mediated signaling were differentially expressed, a number of genes indicated the activation of secondary signaling cascades. Genes related to cytoadherence (cell-cell and cell-matrix), leukocyte extravasation, and inflammatory response were also differentially regulated by treatment, supporting a potential role for 15(S)-HETE in malaria pathogenesis.

Conclusion

These results add insight and detail to 15-HETE's effects on gene expression in macrophage-like cells. Data indicate that while 15-HETE exerts biological activity and may participate in Hz-mediated immuno-modulation, the gene expression changes are modest relative to those altered by the lipid peroxidation product HNE.

Characterization of cerebral malaria in the outbred Swiss Webster mouse infected by Plasmodium berghei ANKA

Plasmodium berghei ANKA (PbA) infection in susceptible inbred mouse strains is the most commonly used experimental model to study pathogenesis of cerebral malaria (CM). Indeed, many concepts on mechanisms related to this complication have arisen from works using this model. Although inbred strains present several advantages and are indicated for most studies, the use of outbred models can show unique usefulness in a number of approaches such as fine post-quantitative trait loci mapping and discovery of genes relevant to CM susceptibility or resistance, as well as pharmacological and vaccine studies. Here we describe the features of PbA infection and CM incidence, and characterize the associated multiorgan pathology in the outbred Swiss Webster mouse. This model showed a sizeable (62.7%) and reproducible incidence of CM demonstrated by clinical signs and histopathological changes in brain (microhaemorrhages, oedema and vessel plugging by mononuclear cells). Major pathological changes were also observed in lungs, liver, thymus and spleen, analogous to those observed in inbred strains. Parasitaemia levels were associated with the risk of CM development, the risk being significantly higher in mice showing higher values of parasitaemia on days 6-7 of infection. This outbred CM model is then suitable for genetic, vaccine and drug studies targeting this malaria complication.

Plasmodium vivax and the importance of the subtelomeric multigene vir superfamily

Plasmodium vivax is responsible for more than 100 million clinical cases yearly. Unlike P. falciparum, in which infected red blood cells cytoadhere via variant proteins, avoiding passage through the spleen, P.-vivax-infected reticulocytes seem not to cytoadhere. However, a variant subtelomeric multigene vir family has been identified in P. vivax. Thus, questions remain about how P. vivax circulates through the spleen and the role of Vir proteins. In this review, the importance of the vir multigene superfamily is reviewed in the light of the completion of the entire genome sequence of P. vivax and from data gathered from experimental infections in reticulocyte-prone non-lethal malaria parasites and natural P. vivax infections.

A genetically hard-wired metabolic transcriptome in Plasmodium falciparum fails to mount protective responses to lethal antifolates

Genome sequences of Plasmodium falciparum allow for global analysis of drug responses to antimalarial agents. It was of interest to learn how DNA microarrays may be used to study drug action in malaria parasites. In one large, tightly controlled study involving 123 microarray hybridizations between cDNA from isogenic drug-sensitive and drug-resistant parasites, a lethal antifolate (WR99210) failed to over-produce RNA for the genetically proven principal target, dihydrofolate reductase-thymidylate synthase (DHFR-TS). This transcriptional rigidity carried over to metabolically related RNA encoding folate and pyrimidine biosynthesis, as well as to the rest of the parasite genome. No genes were reproducibly up-regulated by more than 2-fold until 24 h after initial drug exposure, even though clonal viability decreased by 50% within 6 h. We predicted and showed that while the parasites do not mount protective transcriptional responses to antifolates in real time, P. falciparum cells transfected with human DHFR gene, and adapted to long-term WR99210 exposure, adjusted the hard-wired transcriptome itself to thrive in the presence of the drug. A system-wide incapacity for changing RNA levels in response to specific metabolic perturbations may contribute to selective vulnerabilities of Plasmodium falciparum to lethal antimetabolites. In addition, such regulation affects how DNA microarrays are used to understand the mode of action of antimetabolites.

Traditional knowledge of gene regulation, learned largely from non-pathogenic model organisms such as E. coli, yeast, and mice, suggests that RNA for metabolic pathways are regulated in large part by DNA-binding transcriptional factors that are responsive to cellular metabolic needs. We demonstrate that the malaria-causing Plasmodium falciparum parasites, under lethal drug pressure from an antifolate with a known mechanism of action, are incapable of large reproducible changes in RNA levels for the target pathways, or for any other gene throughout the genome. Small RNA changes, possibly informative of perturbed pathways, can be detected in dying parasites. In addition, significant RNA changes are seen when the hard-wired program, governing RNA levels, itself is altered. Our data formally proves that RNA levels for intermediary metabolism in malaria parasites are largely predetermined. We propose that as a parasite with a complex life cycle travels from one largely predictable intracellular biochemical environment to another, such hard-wiring may be sufficient to manage transcript levels for intermediary metabolism without employing sensory functions. Such a system-wide host–parasite difference in gene regulation may create unexpected pharmacological opportunities when important target pathways are rigid in the parasite but dynamically regulated in host cells.

Systematic gene expression profiling of mouse model series reveals coexpressed genes

A major aim of the Human Brain Proteome Project (HBPP) is a better understanding of the molecular etiology and progression of neurodegenerative diseases. Transgenic and loss-of-function mouse mutant lines (MMLs) serve as experimental models. Transcriptome and proteome regulate each other in a complex and controlled way, and their comparative analysis is an essential aspect. As a fundamental study, we have assessed transcript profiles using a microarray containing 21 000 cDNA probes in a series of disease models within the German Mouse Clinic (GMC). Seventeen distinct organs of one adult stage were systematically collected for each submitted MML. Samples for gene expression profiling are individually selected based on conspicuous phenotypes in at least one of 14 GMC phenotype screens or on previous knowledge of the mutant phenotype. By microarray experiments expression patterns of 90 organs from 46 MMLs were analysed, identifying up to 232 differentially expressed genes in 45 organs. Here we present an overview of the results of all MMLs analysed and demonstrate the efficiency of systematic genome-wide expression profiling for the detection of molecular phenotypes in organs of a mammalian model organism. We identify the recurring regulation of particular genes and groups of coexpressed genes in apparently unrelated MMLs.

Plasmodium falciparum shows transcriptional versatility within the human host

In a recent study published in Nature, Daily et al. profiled parasite gene expression in Plasmodium falciparum infections and identified three in vivo 'states' based on parasite transcription patterns. Despite similar host clinical features, two states displayed highly divergent gene expression, whereas the third was found in individuals with increased inflammatory markers. These findings suggest that parasites exist in different physiological states in vivo, providing an important foundation for future studies investigating how these states might contribute to malaria pathogenesis and outcome.

Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model

Although acute lung injury (ALI) is a common complication of severe malaria, little is known about the underlying molecular basis of lung dysfunction. Animal models have provided powerful insights into the pathogenesis of severe malaria syndromes such as cerebral malaria (CM); however, no model of malaria-induced lung injury has been definitively established. This study used bronchoalveolar lavage (BAL), histopathology and gene expression analysis to examine the development of ALI in mice infected with Plasmodium berghei ANKA (PbA). BAL fluid of PbA-infected C57BL/6 mice revealed a significant increase in IgM and total protein prior to the development of CM, indicating disruption of the alveolar–capillary membrane barrier—the physiological hallmark of ALI. In contrast to sepsis-induced ALI, BAL fluid cell counts remained constant with no infiltration of neutrophils. Histopathology showed septal inflammation without cellular transmigration into the alveolar spaces. Microarray analysis of lung tissue from PbA-infected mice identified a significant up-regulation of expressed genes associated with the gene ontology categories of defense and immune response. Severity of malaria-induced ALI varied in a panel of inbred mouse strains, and development of ALI correlated with peripheral parasite burden but not CM susceptibility. Cd36^−/− mice, which have decreased parasite lung sequestration, were relatively protected from ALI. In summary, parasite burden and CD36-mediated sequestration in the lung are primary determinants of ALI in experimental murine malaria. Furthermore, differential susceptibility of mouse strains to malaria-induced ALI and CM suggests that distinct genetic determinants may regulate susceptibility to these two important causes of malaria-associated morbidity and mortality.

Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) can occur in adult malaria infections with a case fatality rate of 70%–100%. ALI and ARDS are characterized by protein-rich fluid in the lungs, with reduced gas exchange, and in malaria, often accompany high parasite levels and severe or cerebral disease. In this work we have examined lung physiology, pathology and genomics in mouse malaria—Plasmodium berghei ANKA—to show that mice develop malaria-induced ALI. Infected mice have proteinaceous fluid in their lungs, have a migration of inflammatory cells from the blood into the lung walls, and express immune response–related genes. We also found that severity of ALI depended on high parasite levels, both overall and specifically in the lung tissue, but was not consistent with whether the mice developed cerebral malaria. ALI due to Plasmodium berghei ANKA infection models prominent characteristics of human malaria-associated ALI, and we have better defined this model of malaria ALI so it may be used to further explore disease mechanisms and eventual treatment.

C5 deficiency and C5a or C5aR blockade protects against cerebral malaria

Experimental infection of mice with Plasmodium berghei ANKA (PbA) provides a powerful model to define genetic determinants that regulate the development of cerebral malaria (CM). Based on the hypothesis that excessive activation of the complement system may confer susceptibility to CM, we investigated the role of C5/C5a in the development of CM. We show a spectrum of susceptibility to PbA in a panel of inbred mice; all CM-susceptible mice examined were found to be C5 sufficient, whereas all C5-deficient strains were resistant to CM. Transfer of the C5-defective allele from an A/J (CM resistant) onto a C57BL/6 (CM-susceptible) genetic background in a congenic strain conferred increased resistance to CM; conversely, transfer of the C5-sufficient allele from the C57BL/6 onto the A/J background recapitulated the CM-susceptible phenotype. The role of C5 was further explored in B10.D2 mice, which are identical for all loci other than C5. C5-deficient B10.D2 mice were protected from CM, whereas C5-sufficient B10.D2 mice were susceptible. Antibody blockade of C5a or C5a receptor (C5aR) rescued susceptible mice from CM. In vitro studies showed that C5a-potentiated cytokine secretion induced by the malaria product P. falciparum glycosylphosphatidylinositol and C5aR blockade abrogated these amplified responses. These data provide evidence implicating C5/C5a in the pathogenesis of CM.

CXCR3 determines strain susceptibility to murine cerebral malaria by mediating T lymphocyte migration toward IFN-gamma-induced chemokines

Cerebral malaria (CM) results from the binding of infected erythrocytes and leukocytes to brain endothelia. The precise mechanisms underlying lymphocyte recruitment and activation in CM remain unclear. Therefore, the expression of various chemokines was quantified in brains of mice infected with Plasmodium berghei ANKA (PbA). Several chemokines attracting monocytes and activated T-lymphocytes were expressed at high levels. Their expression was almost completely abrogated in IFN-gamma ligand and receptor KO mice, indicating that IFN-gamma is an essential chemokine inducer in vivo. Surprisingly, the expression levels of chemokines, IFN-gamma and also adhesion molecules in the brain were not lower in CM-resistant Balb/c and DBA/2 mice compared to CM-sensitive C57BL/6 and DBA/1 mice, although T lymphocyte sequestration in the brain was significantly less in CM-resistant than in CM-sensitive mice. This difference correlated with a higher up-regulation of the CXC chemokine receptor (CXCR)-3 on splenic T cells and a higher chemotactic response to IFN-gamma-inducible protein-10 (IP-10) in C57BL/6 compared to Balb/c mice. In conclusion, parasite-induced IFN-gamma in the brain results in high local expression levels of specific chemokines for monocytes and lymphocytes. The strain-dependent susceptibility to develop CM is more related to the expression of CXCR3 in circulating leukocytes than to the chemokine expression levels in the brain.

Transcriptomic analysis of the dialogue between Pseudorabies virus and porcine epithelial cells during infection

Background

Transcriptomic approaches are relevant for studying virus-host cell dialogues to better understand the physiopathology of infection and the immune response at the cellular level. Pseudorabies virus (PrV), a porcine Alphaherpesvirus, is a good model for such studies in pig. Since PrV displays a strong tropism for mucous epithelial cells, we developed a kinetics study of PrV infection in the porcine PK15 epithelial cell line. To identify as completely as possible, viral and cellular genes regulated during infection, we simultaneously analyzed PrV and cellular transcriptome modifications using two microarrays i.e. a laboratory-made combined SLA/PrV microarray, consisting of probes for all PrV genes and for porcine genes contained in the Swine Leukocyte Antigen (SLA) complex, and the porcine generic Qiagen-NRSP8 oligonucleotide microarray. We confirmed the differential expression of a selected set of genes by qRT-PCR and flow cytometry.

Results

An increase in the number of differentially expressed cellular genes and PrV genes especially from 4 h post-infection (pi) was observed concomitantly with the onset of viral progeny while no early global cellular shutoff was recorded. Many cellular genes were down-regulated from 4 h pi and their number increased until 12 h pi. UL41 transcripts encoding the virion host shutoff protein were first detected as differentially expressed at 8 h pi. The viral gene UL49.5 encoding a TAP inhibitor protein was differentially expressed as soon as 2 h pi, indicating that viral evasion via TAP inhibition may start earlier than the cellular gene shutoff. We found that many biological processes are altered during PrV infection. Indeed, several genes involved in the SLA class I antigenic presentation pathway (SLA-Ia, TAP1, TAP2, PSMB8 and PSMB9), were down-regulated, thus contributing to viral immune escape from this pathway and other genes involved in apoptosis, nucleic acid metabolism, cytoskeleton signaling as well as interferon-mediated antiviral response were also modulated during PrV infection.

Conclusion

Our results show that the gene expression of both PrV and porcine cells can be analyzed simultaneously with microarrays, providing a chronology of PrV gene transcription, which has never been described before, and a global picture of transcription with a direct temporal link between viral and host gene expression.

Predominance of interferon-related responses in the brain during murine malaria, as identified by microarray analysis

Cerebral malaria (CM) can be a fatal manifestation of Plasmodium falciparum infection. We examined global gene expression patterns during fatal murine CM (FMCM) and noncerebral malaria (NCM) by microarray analysis. There was differential expression of a number of genes, including some not yet characterized in the pathogenesis of FMCM. Some gene induction was observed during Plasmodium berghei infection regardless of the development of CM, and there was a predominance of genes linked to interferon responses, even in NCM. However, upon real-time PCR validation and quantitation, these genes were much more highly expressed in FMCM than in NCM. The observed changes included genes belonging to pathways such as interferon signaling, major histocompatibility complex processing and presentation, apoptosis, and immunomodulatory and antimicrobial processes. We further characterized differentially expressed genes by examining the cellular source of their expression as well as their temporal expression patterns during the course of malaria infection. These data identify a number of novel genes that represent interesting candidates for further investigation in FMCM.