Study Of Host-pathogen Interactions Research Articles

Physical Extraction and Fast Protein Liquid Chromatography for Purifying Flagella Filament From Uropathogenic Escherichia coli for Immune Assay.

Flagella are expressed on the surface of a wide range of bacteria, conferring motility and contributing to virulence and innate immune stimulation. Host-pathogen interaction studies of the roles of flagella in infection, including due to uropathogenic Escherichia coli (UPEC), have used various methods to purify and examine the biology of the major flagella subunit protein, FliC. These studies have offered insight into the ways in which flagella proteins interact with host cells. However, previous methods used to extract and purify FliC, such as mechanical shearing, ultracentrifugation, heterologous expression in laboratory E. coli strains, and precipitation-inducing chemical treatments have various limitations; as a result, there are few observations based on highly purified, non-denatured FliC in the literature. This is especially relevant to host-pathogen interaction studies such as immune assays that are designed to parallel, as closely as possible, naturally-occurring interactions between host cells and flagella. In this study, we sought to establish a new, carefully optimized method to extract and purify non-denatured, native FliC from the reference UPEC strain CFT073 to be suitable for immune assays. To achieve purification of FliC to homogeneity, we used a mutant CFT073 strain containing deletions in four major chaperone-usher fimbriae operons (type 1, F1C and two P fimbrial gene clusters; CFT073Δ4). A sequential flagella extraction method based on mechanical shearing, ultracentrifugation, size exclusion chromatography, protein concentration and endotoxin removal was applied to CFT073Δ4. Protein purity and integrity was assessed using SDS-PAGE, Western blots with anti-flagellin antisera, and native-PAGE. We also generated a fliC-deficient strain, CFT073Δ4ΔfliC, to enable the concurrent preparation of a suitable carrier control to be applied in downstream assays. Innate immune stimulation was examined by exposing J774A.1 macrophages to 0.05-1 μg of purified FliC for 5 h; the supernatants were analyzed for cytokines known to be induced by flagella, including TNF-α, IL-6, and IL-12; the results were assessed in the context of prior literature. Macrophage responses to purified FliC encompassed significant levels of several cytokines consistent with prior literature reports. The purification method described here establishes a new approach to examine highly purified FliC in the context of host-pathogen interaction model systems.

New Age Strategies To Reconstruct Mucosal Tissue Colonization and Growth in Cell Culture Systems.

Over the past few decades, in vitro cell culture systems have greatly expanded our understanding of host-pathogen interactions. However, studies using these models have been limited by the fact that they lack the complexity of the human body. Therefore, recent efforts that allow tissue architecture to be mimicked during in vitro culture have included the development of methods and technology that incorporate tissue structure, cellular composition, and efficient long-term culture. These advances have opened the door for the study of pathogens that previously could not be cultured and for the study of pathophysiological properties of infection that could not be easily elucidated using traditional culture models. Here we discuss the latest studies using organoids and engineering technology that have been developed and applied to the study of host-pathogen interactions in mucosal tissues.

A bilayer tissue culture model of the bovine alveolus

The epithelial lining of the lung is often the first point of interaction between the host and inhaled pathogens, allergens and medications. Epithelial cells are therefore the main focus of studies which aim to shed light on host-pathogen interactions, to dissect the mechanisms of local host immunity and study toxicology. If these studies are not to be conducted exclusively in vivo, it is imperative that in vitro models are developed with a high in vitro-in vivo correlation. We describe here a co-culture bilayer model of the bovine alveolus, designed to overcome some of the limitations encountered with mono-culture and live animal models. Our system includes bovine pulmonary arterial endothelial cells (BPAECs) seeded onto a permeable membrane in 24 well Transwell format. The BPAECs are overlaid with immortalised bovine alveolar type II epithelial cells and the bilayer cultured at air-liquid interface for 14 days before use; in our case to study host-mycobacterial interactions. Characterisation of novel cell lines and the bilayer model have provided compelling evidence that immortalised bovine alveolar type II cells are an authentic substitute for primary alveolar type II cells and their culture as a bilayer in conjunction with BPAECs provides a physiologically relevant in vitro model of the bovine alveolus. The bilayer model may be used to study dynamic intracellular and extracellular host-pathogen interactions, using proteomics, genomics, live cell imaging, in-cell ELISA and confocal microscopy. The model presented in this article enables other researchers to establish an in vitro model of the bovine alveolus that is easy to set up, malleable and serves as a comparable alternative to in vivo models, whilst allowing study of early host-pathogen interactions, currently not feasible in vivo. The model therefore achieves one of the 3Rs objectives in that it replaces the use of animals in research of bovine respiratory diseases.

The greater wax moth, Galleria mellonella to study host-pathogen interactions

The massive use of antibiotics in health and agriculture has led to the emergence of pathogenic microorganisms resistant to frequently used treatments. In 2017, the World Health Organization (WHO) published its first ever list of antibiotic-resistant "priority pathogens", a catalogue of twelve families of bacteria that pose the greatest threat to human health. In this context, a new model for the study of host-pathogen interactions is becoming increasingly popular : the greater wax moth, Galleria mellonella. This butterfly larvae, sometimes considered as a new "laboratory rat", has many practical advantages and is an important host in the study of some steps in the pathogenicity of infectious agents and the identification of new treatments. This review presents this alternative model and describes its possible applications.

Meta-analysis suggests evidence of novel stress-related pathway components in Orsay virus - Caenorhabditis elegans viral model

The genetic model organism, Caenorhabditis elegans (C. elegans), shares many genes with humans and is the best-annotated of the eukaryotic genome. Therefore, the identification of new genes and pathways is unlikely. Nevertheless, host-pathogen interaction studies from viruses, recently discovered in the environment, has created new opportunity to discover these pathways. For example, the exogenous RNAi response in C. elegans by the Orsay virus as seen in plants and other eukaryotes is not systemic and transgenerational, suggesting different RNAi pathways between these organisms. Using a bioinformatics meta-analysis approach, we show that the top 17 genes differentially-expressed during C. elegans infection by Orsay virus are functionally uncharacterized genes. Furthermore, functional annotation using similarity search and comparative modeling, was able to predict folds correctly, but could not assign easily function to the majority. However, we could identify gene expression studies that showed a similar pattern of gene expression related to toxicity, stress and immune response. Those results were strengthened using protein-protein interaction network analysis. This study shows that novel molecular pathway components, of viral innate immune response, can be identified and provides models that can be further used as a framework for experimental studies. Whether these features are reminiscent of an ancient mechanism evolutionarily conserved, or part of a novel pathway, remain to be established. These results reaffirm the tremendous value of this approach to broaden our understanding of viral immunity in C. elegans.

Unraveling the host's immune response to infection: Seeing is believing.

It has long been appreciated that understanding the interactions between the host and the pathogens that make us sick is critical for the prevention and treatment of disease. As antibiotics become increasingly ineffective, targeting the host and specific bacterial evasion mechanisms are becoming novel therapeutic approaches. The technology used to understand host‐pathogen interactions has dramatically advanced over the last century. We have moved away from using simple in vitro assays focused on single‐cell events to technologies that allow us to observe complex multicellular interactions in real time in live animals. Specifically, intravital microscopy (IVM) has improved our understanding of infection, from viral to bacterial to parasitic, and how the host immune system responds to these infections. Yet, at the same time it has allowed us to appreciate just how complex these interactions are and that current experimental models still have a number of limitations. In this review, we will discuss the advances in vivo IVM has brought to the study of host‐pathogen interactions, focusing primarily on bacterial infections and innate immunity.

Effects of intratracheal Fusarium solani inoculation in immunocompetent mice

Fusariosis is an infection that is caused by fungi of the Fusarium genus. It is the second most common fungus that is associated with human fungal infections, usually in immunocompromised individuals. The incidence of such infections has been increasing, including in immunocompetent hosts. Studies of host-pathogen interactions are scarce, and the pathophysiology of the disease is unknown. One limitation of such studies is the lack of adequate techniques for mammalian infection, in which no standardized protocols have been established with fungi with a focus on the respiratory tract. The aim of the present study was to assess the first 24 h of infection after the intratracheal inoculation of F. solani microconidia in immunocompetent mice. Colony-forming units (CFU) were counted, and histopathological analysis was performed. Under conditions of high fungal burden, F. solani caused lethal tissue damage in the lungs. Under conditions of low fungal burden, the infection was not lethal, but several alterations of pulmonary tissue and the presence of the fungus in the lungs were observed. No evidence of fungal dissemination was found in the kidneys, spleen, liver, or heart 24 h after infection. The present intratracheal model effectively established fungal infection and appears to be suitable for studies of Fusarium spp.

Bioinformatic Tools and Genome Analysis of Citrus tristeza virus.

High-throughput sequencing (HTS) is a powerful tool employed by plant virologists for the detection of viruses, the characterization of virus genomes and the study of host-pathogen interactions. Virus detection has been an important application of this technology, which has resulted in the discovery of novel viruses or viral strains as well as for the detection of knownviruses in a plant sample. Here we describe the entire process that needs to be considered for the genome analysis of Citrus tristeza virus (CTV) by HTS, including the experimental design, sample preparation, nucleic acid purification, HTS library construction, and bioinformatic analysis.

Dual Analysis of Virus-Host Interactions: The Case of Ostreid herpesvirus 1 and the Cupped Oyster Crassostrea gigas

Dual analyses of the interactions between Ostreid herpesvirus 1 (OsHV-1) and the bivalve Crassostrea gigas during infection can unveil events critical to the onset and progression of this viral disease and can provide novel strategies for mitigating and preventing oyster mortality. Among the currently used “omics” technologies, dual transcriptomics (dual RNA-seq) coupled with the analysis of viral DNA in the host tissues has greatly advanced the knowledge of genes and pathways mostly contributing to host defense responses, expression profiles of annotated and unknown OsHV-1 open reading frames (ORFs), and viral genome variability. In addition to dual RNA-seq, proteomics and metabolomics analyses have the potential to add complementary information, needed to understand how a malacoherpesvirus can redirect and exploit the vital processes of its host. This review explores our current knowledge of “omics” technologies in the study of host-pathogen interactions and highlights relevant applications of these fields of expertise to the complex case of C gigas infections by OsHV-1, which currently threaten the mollusk production sector worldwide.

Microglia Increase Inflammatory Responses in iPSC-Derived Human BrainSpheres.

Human induced pluripotent stem cells (iPSCs), together with 21st century cell culture methods, have the potential to better model human physiology with applications in toxicology, disease modeling, and the study of host-pathogen interactions. Several models of the human brain have been developed recently, demonstrating cell-cell interactions of multiple cell types with physiologically relevant 3D structures. Most current models, however, lack the ability to represent the inflammatory response in the brain because they do not include a microglial cell population. Microglia, the resident immunocompetent phagocytes in the central nervous system (CNS), are not only important in the inflammatory response and pathogenesis; they also function in normal brain development, strengthen neuronal connections through synaptic pruning, and are involved in oligodendrocyte and neuronal survival. Here, we have successfully introduced a population of human microglia into 3D human iPSC-derived brain spheres (BrainSpheres, BS) through co-culturing cells of the Immortalized Human Microglia – SV40 cell line with the BS model (μBS). We detected an inflammatory response to lipopolysaccharides (LPS) and flavivirus infection, which was only elicited in the model when microglial cells were present. A concentration of 20 ng/mL of LPS increased gene expression of the inflammatory cytokines interleukin-6 (IL-6), IL-10, and IL-1β, with maximum expression at 6–12 h post-exposure. Increased expression of the IL-6, IL-1β, tumor necrosis factor alpha (TNF-α), and chemokine (C-C motif) ligand 2 (CCL2) genes was observed in μBS following infection with Zika and Dengue Virus, suggesting a stronger inflammatory response in the model when microglia were present than when only astrocyte, oligodendrocyte, and neuronal populations were represented. Microglia innately develop within cerebral organoids (Nature communications)1, our findings suggest that the μBS model is more physiologically relevant and has potential applications in infectious disease and host-pathogen interactions research.

Editorial introductions

Current Opinion in Critical Care was launched in 1995. It is one of a successful series of review journals whose unique format is designed to provide a systematic and critical assessment of the literature as presented in the many primary journals. The field of critical care is divided into 13 sections that are reviewed once a year. Each section is assigned a Section Editor, a leading authority in the area, who identifies the most important topics at that time. Here we are pleased to introduce the journal's Section Editors for this issue. SECTION EDITORS Thomas RimmeléThomas RimmeléProf. Thomas Rimmelé is the Chairman of the Department of Anaesthesiology and Intensive Care Medicine at Edouard Herriot Hospital, Lyon, France, and Chairman of the Department of Organ Harvest Coordination for the Hospices Civils de Lyon, France. He gained his medical degree in 2004, specialising in anaesthesiology and intensive care, from the Claude Bernard University, Lyon, France, and subsequently completed a PhD on extracorporeal blood purification therapies in sepsis. In addition to blood purification for sepsis, Prof. Rimmelé's academic interests include acute kidney injury, renal replacement therapy in the intensive care unit, and simulation in healthcare as he is also the co-director of the simulation center at Lyon University, France. Prof. Rimmelé is the author or co-author of more than 150 peer-reviewed articles or book chapters and regularly delivers lectures at international meetings. Wesley H. SelfWesley H. SelfDr Wesley H. Self, MD, MPH, is the Vice Chair for Research in the Department of Emergency Medicine at Vanderbilt University Medical Center in Nashville, Tennessee, USA. He is an emergency physician and clinical researcher focused on the intersection of emergency and critical care medicine. He has authored over 100 peer-reviewed publications and widely lectured and presented research findings on the early management of pneumonia, sepsis, and related emergencies. Dr Self was the principal investigator for the Saline Against Lactated Ringer's or Plasmalyte in the Emergency Department (SALT-ED) trial (N Engl J Med 2018), which demonstrated a lower incidence of major adverse kidney events following IV fluid resuscitation with balanced crystalloids compared with saline. He was also a lead investigator in the Etiology of Pneumonia in the Community (EPIC) study (N Engl J Med 2015), which demonstrated a high disease burden from respiratory viruses among patients hospitalized with community-acquired pneumonia in the United States. Dr Self serves as the co-principal investigator of the Vanderbilt Clinical Center in the Prevention and Early Treatment of Acute Lung Injury (PETAL) Clinical Trials Network (www.petalnet.org) funded by the National Heart, Lung and Blood Institute (NHLBI). His current work focuses on embedding pragmatic comparative effectiveness trials into ongoing clinical care to learn how to improve early resuscitation. Dr Self completed medical school at the University of Virginia, USA, residency training in emergency medicine at Northwestern University, USA, and a clinical research fellowship at Vanderbilt University, USA. He is currently an Associate Professor of Emergency Medicine at Vanderbilt University Medical Center, where he leads the Division of Emergency Medicine Research. Karim AsehnouneKarim AsehnouneProf. Karim Asehnoune got his degree as an MD in 1999 at University René Descartes Paris, France. After completing his PhD in immunology in 2001, he spent one year in the lab of Prof. Edward Abraham in the University of Colorado, Denver, USA (2002). He was appointed Professor of Anaesthesiology and Critical Care Medicine in the University of Nantes, France, in 2009. Prof. Asehnoune is the head of the Anaesthesiology department of Hospital Hotel-Dieu, and the director of the 30-bed surgical Intensive Care Unit at the University hospital of Nantes, France. He is currently a member of the scientific committee of the French Society of Anaesthesiology and Critical Care Medicine, and the director of a French network of ICUs (www.ATLANREA.org). Professor Asehnoune was involved as the coordinator of several multi-centre trials, and he was the primary investigator of 2 multicentre double blind randomised studies evaluating corticosteroids in severe trauma patients. He is the director of a lab dedicated to the study of host-pathogen interactions (http://www.ea3826.univ-nantes.fr/). He has published more than 180 peer-reviewed articles.

The Expanding Molecular Genetics Tool Kit in Chlamydia.

Chlamydia has emerged as an important model system for the study of host pathogen interactions, in part due to a resurgence in the development of tools for its molecular genetic manipulation. An additional tool, published by Keb et al. (G. Keb, R. Hayman, and K. A. Fields, J. Bacteriol. 200:e00479-18, 2018, https://doi.org/10.1128/JB.00479-18), now allows for custom genetic engineering of genomic regions that were traditionally recalcitrant to genetic manipulation, such as genes within operons. This new method will be an essential instrument for the elucidation of Chlamydia-host interactions.

The Host Microbiota Contributes to Early Protection Against Lung Colonization by Mycobacterium tuberculosis.

Tuberculosis (TB), caused by the airborne bacterial pathogen Mycobacterium tuberculosis, remains a major source of morbidity and mortality worldwide. So far, the study of host-pathogen interactions in TB has mostly focused on the physiology and virulence of the pathogen, as well as, on the various innate and adaptive immune compartments of the host. Microbial organisms endogenous to our body, the so-called microbiota, interact not only with invading pathogens, but also with our immune system. Yet, the impact of the microbiota on host defense against M. tuberculosis remains poorly understood. In order to address this question, we adapted a robust and reproducible mouse model of microbial dysbiosis based on a combination of wide-spectrum antibiotics. We found that microbiota dysbiosis resulted in an increased early colonization of the lungs by M. tuberculosis during the first week of infection, correlating with an altered diversity of the gut microbiota during this time period. At the cellular level, no significant difference in the recruitment of conventional myeloid cells, including macrophages, dendritic cells and neutrophils, to the lungs could be detected during the first week of infection between microbiota-competent and -deficient mice. At the molecular level, microbiota depletion did not impact the global production of pro-inflammatory cytokines, such as interferon (IFN)γ, tumor necrosis factor (TNF)α and interleukin (IL)-1β in the lungs. Strikingly, a reduced number of mucosal-associated invariant T (MAIT) cells, a population of innate-like lymphocytes whose development is known to depend on the host microbiota, was observed in the lungs of the antibiotics-treated animals after 1week of infection. These cells produced less IL-17A in antibiotics-treated mice. Notably, dysbiosis correction through the inoculation of a complex microbiota in antibiotics-treated animals reversed these phenotypes and improved the ability of MAIT cells to proliferate. Altogether, our results demonstrate that the host microbiota contributes to early protection of lung colonization by M. tuberculosis, possibly through sustaining the function(s) of MAIT cells. Our study calls for a better understanding of the impact of the microbiota on host-pathogen interactions in TB. Ultimately, this study may help to develop novel therapeutic approaches based on the use of beneficial microbes, or components thereof, to boost anti-mycobacterial immunity.

Generation of mouse-zebrafish hematopoietic tissue chimeric embryos for hematopoiesis and host-pathogen interaction studies.

ABSTRACTXenografts of the hematopoietic system are extremely useful as disease models and for translational research. Zebrafish xenografts have been widely used to monitor blood cancer cell dissemination and homing due to the optical clarity of embryos and larvae, which allow unrestricted in vivo visualization of migratory events. Here, we have developed a xenotransplantation technique that transiently generates hundreds of hematopoietic tissue chimeric embryos by transplanting murine bone marrow cells into zebrafish blastulae. In contrast to previous methods, this procedure allows mammalian cell integration into the fish developmental hematopoietic program, which results in chimeric animals containing distinct phenotypes of murine blood cells in both circulation and the hematopoietic niche. Murine cells in chimeric animals express antigens related to (i) hematopoietic stem and progenitor cells, (ii) active cell proliferation and (iii) myeloid cell lineages. We verified the utility of this method by monitoring zebrafish chimeras during development using in vivo non-invasive imaging to show novel murine cell behaviors, such as homing to primitive and definitive hematopoietic tissues, dynamic hematopoietic cell and hematopoietic niche interactions, and response to bacterial infection. Overall, transplantation into the zebrafish blastula provides a useful method that simplifies the generation of numerous chimeric animals and expands the range of murine cell behaviors that can be studied in zebrafish chimeras. In addition, integration of murine cells into the host hematopoietic system during development suggests highly conserved molecular mechanisms of hematopoiesis between zebrafish and mammals.This article has an associated First Person interview with the first author of the paper.

Temperature affects the biology of Schmidtea mediterranea

Studies of tissue regeneration and host-pathogen interactions using the model planarian Schmidtea mediterranea have been performed at an experimental temperature of 19 °C. S. mediterranea planarians exposed to 19 °C–32 °C were observed for survival, mobility, feeding and regeneration for three months and elimination of the Staphylococcus aureus pathogen over six days. S. mediterranea planarians died at 30 °C–32 °C after 18 days of observation but tolerated temperatures of 19 °C up to 28 °C with non-significant differences in mobility and feeding behavior. Genetic malleability tested by RNAi feeding was still efficient at 26 °C and 28 °C. Concerning the immune capacity of planarians, we reported an exacerbation of the immune response in worms infected by S. aureus at 26 °C and 28 °C. These observations suggest a temperature modulation of planarian stem cells and illustrate the importance of modulating experimental temperature when using planarians as model organisms to study regeneration and immune response.

An Unbiased Screen for Human Cytomegalovirus Identifies Neuropilin-2 as a Central Viral Receptor

Characterizing cell surface receptors mediating viral infection is critical for understanding viral tropism and developing antiviral therapies. Nevertheless, due to challenges associated with detecting protein interactions on the cell surface, the host receptors of many human pathogens remain unknown. Here, we build a library consisting of most single transmembrane human receptors and implement a workflow for unbiased and high-sensitivity detection of receptor-ligand interactions. We apply this technology to elucidate the long-sought receptor of human cytomegalovirus (HCMV), the leading viral cause of congenital birth defects. We identify neuropilin-2 (Nrp2) as the receptor for HCMV-pentamer infection in epithelial/endothelial cells and uncover additional HCMV interactors. Using a combination of biochemistry, cell-based assays, and electron microscopy, we characterize the pentamer-Nrp2 interaction and determine the architecture of the pentamer-Nrp2 complex. This work represents an important approach to the study of host-pathogen interactions and provides a framework for understanding HCMV infection, neutralization, and the development of novel anti-HCMV therapies.

A survey to examine Candida albicans transmission through yolk sac and amniotic sac in chicken embryos

Candida albicans is the fungus responsible for the incidence of candidiasis. This fungus, in low volumes, is a natural inhabitant in various organs of birds which can act as a pathogen in some circumstances. Infection patterns are used to study microbial pathogenesis. The infection patterns can be used in the evaluation of host-pathogen interaction, pathogenicity, virulence agents, and remedy studies. In order to eliminate the diversity and differences of the infection patterns between invertebrates and mice, this study introduced an alternative, low-cost, and simple application of infection patterns for Candida albicans based on embryonated eggs. Similar to other infection patterns, embryonated eggs can be used as an acceptable pattern to study fungal pathogenesis. In this study, systemic candidiasis was achieved in chicken embryos by yolk sac and amniotic sac inoculations of Candida albicans and its histopathological demonstrations were examined in three organs including liver, kidney, and lung. Candida albicans was subcultured once on yeast extract-peptone-dextrose (YPD) agar. Plating serial dilutions on YPD agar plates was carried out to confirm the infectious doses. Subsequently, inoculation into yolk sac and amniotic sac was carried out with the intended infectious dose. After 18 days of incubation, histopathologic specimens were taken from embryonated chicken organs. Predominant lesions were observed in liver, kidney, and lung which included the accumulation of mononuclear cells. In conclusion, this study corroborated the embryo transmission of Candida albicans via yolk sack and amniotic routes by focusing on the importance of hygiene and biosecurity in breeder flocks and particularly in hatcheries.

Environmentally persistent pathogens present unique challenges for studies of host-pathogen interactions: Reply to Field (2018).

Linked article: https://doi.org/10.1002/ece3.4034

Quantification of Bioorthogonal Stability in Immune Phagocytes Using Flow Cytometry Reveals Rapid Degradation of Strained Alkynes.

One of the areas in which bioorthogonal chemistry—chemistry performed inside a cell or organism—has become of pivotal importance is in the study of host–pathogen interactions. The incorporation of bioorthogonal groups into the cell wall or proteome of intracellular pathogens has allowed study within the endolysosomal system. However, for the approach to be successful, the incorporated bioorthogonal groups must be stable to chemical conditions found within these organelles, which are some of the harshest found in metazoans: the groups are exposed to oxidizing species, acidic conditions, and reactive thiols. Here we present an assay that allows the assessment of the stability of bioorthogonal groups within host cell phagosomes. Using a flow cytometry-based assay, we have quantified the relative label stability inside dendritic cell phagosomes of strained and unstrained alkynes. We show that groups that were shown to be stable in other systems were degraded by as much as 79% after maturation of the phagosome.

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

SUMMARYTranscriptomics, 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.