Epigenetics of Host–Pathogen Interactions: The Road Ahead and the Road Behind

Summary

A growing body of evidence points towards epigenetic mechanisms being responsible for a wide range of biological phenomena, from the plasticity of plant growth and development to the nutritional control of caste determination in honeybees and the etiology of human disease (e.g., cancer). With the (partial) elucidation of the molecular basis of epigenetic variation and the heritability of certain of these changes, the field of evolutionary epigenetics is flourishing. Despite this, the role of epigenetics in shaping host–pathogen interactions has received comparatively little attention. Yet there is plenty of evidence supporting the implication of epigenetic mechanisms in the modulation of the biological interaction between hosts and pathogens. The phenotypic plasticity of many key parasite life-history traits appears to be under epigenetic control. Moreover, pathogen-induced effects in host phenotype may have transgenerational consequences, and the bases of these changes and their heritability probably have an epigenetic component. The significance of epigenetic modifications may, however, go beyond providing a mechanistic basis for host and pathogen plasticity. Epigenetic epidemiology has recently emerged as a promising area for future research on infectious diseases. In addition, the incorporation of epigenetic inheritance and epigenetic plasticity mechanisms to evolutionary models and empirical studies of host–pathogen interactions will provide new insights into the evolution and coevolution of these associations. Here, we review the evidence available for the role epigenetics on host–pathogen interactions, and the utility and versatility of the epigenetic technologies available that can be cross-applied to host–pathogen studies. We conclude with recommendations and directions for future research on the burgeoning field of epigenetics as applied to host–pathogen interactions.

What Is Epigenetics?

Few areas in biology attract as much current attention and yet require as much presentation as the field of epigenetics. The term “epigenetics” was first used by Waddington to describe the process through which genotypes give rise to phenotypes during development [1]. Since then, there has been a burgeoning interest in the field of epigenetics that has been coupled with a diversification in the use of the term: epigenetics means different things to the different fields of biology, and even within a given field, different authors may use it in somewhat different contexts, generating a great deal of confusion in the process [2]. Broadly speaking, epigenetics refers to stimuli-triggered changes in gene expression due to processes that arise independent of changes in the underlying DNA sequence. Some of these processes have been elucidated and include DNA methylation [3], histone modifications and chromatin-remodeling proteins [4], and DNA silencing by noncoding RNAs (ncRNA) (BOX 1) [5]. This general definition of “epigenetics” is, however, used in two broadly different contexts. For some authors, the term “epigenetics” includes all transient changes in gene expression that occur at the individual cell level, as well as those that are propagated during mitosis in multicellular organisms and remain stable at the time scale of an individual (Figure 1). For clarity, we refer to this as epigenetic plasticity (see [6]). A good example is the development of morphologically different castes of bees from genetically identical individuals through nutritionally triggered DNA methylation [7]. Yet for other authors, and most notably for evolutionary biologists, the term epigenetics refers exclusively to epigenetic inheritance: the stimuli-triggered variation in gene expression that is heritable across generations. Here, the epigenetic changes are generated in the germ line in multicellular organisms (either directly or indirectly, see Jablonka and Raz [8]) or maintained clonally in single-cell organisms (Figure 1) [8], [9]. A classic example of transgenerational epigenetic inheritance involves a change in flower symmetry from bilateral to radial in Linaria vulgaris, which relates to different levels of methylation of the gene Lcyc [10]. In this review, we contend that both epigenetic plasticity and epigenetic inheritance are important in shaping host–pathogen interactions, and thus we use the term “epigenetics” to encompass both of these definitions.

Epigenetics of Host–Pathogen Interactions

In recent years, a plethora of papers on the role of epigenetic phenomena on gene expression and phenotype have brought about enormous progress in other fields (such as cancer epigenetics [11]) thanks in part to the significant advances of epigenetic technologies (see Box 2 and Table S1). Conversely, we still know comparatively little about the extent and significance of epigenetic variation in host–pathogen interactions (Figure 2).

Host–pathogen interactions are amongst the most plastic and dynamic systems in nature. To cope with the selective constraints imposed by their hosts, many pathogens have evolved an unparalleled level of phenotypic plasticity in their life history traits [12]. Likewise, the host phenotype is drastically and rapidly altered by the presence of a pathogen, and in some cases, the parasitized phenotype is inherited across host generations (see [13] for a review). In addition, co-adaptations between hosts and pathogens often occur over such short evolutionary time scales as to call into question the sole role of genetic modifications (i.e., mutation and/or recombination) as an underlying mechanism [14]. In this sense, epigenetic modifications may provide an accessory source of fast-acting, reversible, and readily available phenotypic variation that can be directly shaped by both host and pathogen selection pressures (Figure 3) [9], [14].

We describe herein recent examples of host–pathogen studies where epigenetic processes have already been shown to play a role and which can be broadly classified into (1) pathogen plasticity and (2) pathogen-induced alterations of the host (Table 1).

Pathogen Plasticity

One of the most notorious aspects of pathogens is the morphological and developmental plasticity they exhibit, which is intimately linked to their survival and transmission in the host. Complex life-history transitions that occur in response to the changing host environment require rapid and profound alterations of their gene expression profiles. Take, for example, the malaria parasites in the genus Plasmodium. In the vertebrate host, the parasite has distinct hepatocytic and erythrocytic stages, and it forms sexually differentiated gametocytes in the blood that are taken up by the mosquito, where these gametocytes mate, then migrate through the midgut to form oocysts and from there to the salivary glands as sporozoites. Previous studies have revealed distinct gene expression profiles in all of these phases (reviewed in [15]), suggesting that developmental switches are transcriptionally regulated. However, apicomplexan parasites such as Plasmodium are notoriously poor in transcription factors [16]. In contrast, these parasites contain a rich repertoire of histone variants, chromatin and histone modifying enzymes, and RNA-mediated silencing mechanisms [17], [18]. In Toxoplasma gondii, histone acetylation has been shown to be responsible for the switch between the replicative and nonreplicative stages of the pathogen [19], [20]. Similar mechanisms of epigenetic regulation have been characterized in other protists (Table 1). Although less studied, Trypanosoma brucei is the only Apicomplexa where DNA methylation has been detected, but the significance of these epigenetic modifications in parasite cell-cycle regulation remains unexplored [18]. More recently, DNA methylation has been shown to be responsible for the transition between the yeast and hyphal forms of the polymorphic yeast Candida albicans [21].

The second striking aspect of pathogen plasticity concerns their ability to alter the expression of genes linked to virulence processes, which allows them to colonize, replicate, and/or disseminate within the host. Within the Apicomplexa, Plasmodium falciparum switches its variant surface proteins during its erythrocytic stage to avoid the host's immune system (antigenic variation). These surface proteins are encoded by highly polymorphic gene families (var, rif, stevor, and pfmc-2tm, among others). In the case of the var family, the ability of the parasite to express only one of the 60 genes that encode for these proteins (called PfEMP1) is epigenetically regulated through histone modifications [22]. In a very recent study, Rovira-Graells et al. [23] have reported a more general association between these histone and chromatin marks and clonally variant expression, extending previous results on Plasmodium var genes to all but two of the 28 variantly expressed gene families. In addition, recent work has shown that the epigenetic state of the parasite is maintained during several rounds of cell division [24]. Epigenetic control of virulence factors is well demonstrated in several microbial pathogens. In Entamoeba histolitica, for example, histone methylation and demethylation regulate the expression of the amoebapore protein (a protein responsible for the cytotoxicity of the pathogen [25]). DNA methylation is also an essential regulatory mechanism of virulence in several pathogenic bacteria [26], [27]. In Salmonella enterica, for example, lack of Dam (DNA adenine methyltransferase) methylation causes, amongst other things, envelope instability, reduced motility, and an impaired ability to invade the intestinal epithelium [28].

Given the importance of epigenetics for pathogen biology, understanding how the host environment cues the epigenetic transition between the replicative and transmission stages and the virulence factors of morbid and deadly parasites such as Plasmodium is not only an academic exercise, but it will also provide novel targets for drug development; an option that has been termed “epigenetic therapy” is currently being tested in clinical trials for other (noninfectious) diseases. These prevention and treatment strategies translated to the field of host–parasite interactions could be aimed at arresting the developmental switches of parasites within the host or at blocking or limiting their virulence. This could be achieved by using chemical inhibitors, gene knockout, and RNA interference (RNAi) approaches, designed to target the epigenetic machinery of the parasite such as the DNA methyltransferases or the chromatin and histone modifying enzymes (see Table 1, [29]).

Pathogen-Induced Alterations of the Host

Pathogen-induced alterations of host physiology, morphology, and behavior are widely documented in the scientific literature. Perhaps the most fascinating examples of these changes are those that have been shown to be the result of a manipulative strategy of the pathogen aimed at maximizing its survival and transmission. Although some of the mechanisms underlying such pathogen manipulation have been unraveled [30]–[32], by and large, we know startlingly little of the strategies used by pathogens to achieve this end. In the last few years, however, evidence has accumulated that histone modifications and chromatin remodeling regulate gene expression and are thus key targets for pathogen manipulation during an infection [33]. One such obvious target is the host's immune system. In recent years, the epigenetic modulation of host's transcriptional program linked to host defense genes has emerged as a relatively common occurrence of pathogenic viral and bacterial infections [33], [34]. Bacteria are the hallmark of epigenetic studies on microbes and provide several pioneer examples on infection-induced host gene reprogramming [32]. A diverse array of bacterial effectors has been identified that either mimic or inhibit the host cellular machinery, thus facilitating the pathogen's life-cycle. MAPK (mitogen-activated protein kinase), Interferon (IFN), and transcription factor NF-κB signaling pathways are common targets of bacterial-induced post-translational modifications, acetylation, ubiquitylation, and phosphorylation on histones and chromatin-associated proteins [35]. Within the alveolar macrophages, Mycobacterium tuberculosis, for example, inhibits interferon-γ-induced expression of several immune genes through histone acetylation [36], which explains the persistence of long-term chronic tuberculosis infections in some patients. This mechanism is not restricted to bacteria but appears rather ubiquitous among intracellular pathogens (Table 1). Influenza viruses go a step further at circumventing host immune defenses. In a recent study, Marazzi et al. [37] report an influenza protein called NS1 that contains an amino-acid sequence (ARTK) very similar to the host's H3 histone tail. The authors provide compelling evidence of how using this histone mimic sequence, the viral NS1 protein hijacks a host transcription elongation factor (hPAF1), selectively suppressing the cell's production of antiviral proteins. This work is a good example of how a molecule of pathogen origin can directly induce an epigenetic modification in the host. More studies are needed that establish causative relationships between the pathogen infection and host epigenetic modifications such as DNA methylation and posttranslational histone modifications. Indeed, most of the evidence currently available is correlational (but see Table 1), and cases where proteins of pathogen origin have been shown to interact directly with the host epigenetic machinery are still scarce.

An additional characteristic of many pathogens is their ability to manipulate the reproductive biology of their hosts. The endobacteria Wolbachia pipientis is the archetypal example of such reproductive manipulations. Wolbachia is the most common parasitic microorganism in insects. Its maternal inheritance has selected for a variety of phenotypes associated with manipulating the reproduction of its hosts: forcing asexuality, feminizing hosts, killing males, and inducing incompatibility between infected males and uninfected (or differently infected) females [38]. Negri et al. [39] have provided the first evidence that a feminizing strain of Wolbachia interferes with the genetic imprinting of its host (the leafhopper Zyginidia pullula) by altering the host's methylation pattern. Recently, the widespread existence of putative DNA-methyltransferases in the prophage of the Wolbachia infecting several Drosophila species [40] has raised the possibility that this may be a widespread mechanism of epigenetic interference in this endosymbiotic bacteria. The link is, however, unclear since these enzymes have been identified as adenine methyltransferases, a family of prokaryotic enzymes that methylate the amino group at the C-6 position of adenines, whereas in the example reported above, genetic imprinting of the invertebrate host seems to occur at the C-5 carbon of CpG cytosines.

Not all modifications that take place in the infected host are, however, adaptive for the pathogen. Some of them are adaptive strategies of the host aimed to compensate or minimize the effects of the infection. In vertebrates, invertebrates, and plants, individuals that have recovered from certain infectious diseases are protected against later infection with those same diseases (immune priming). While the mechanistic basis of immune priming in invertebrates is still unresolved, in vertebrates, histone modifications may be associated with immune memory following a viral infection in CD8 T cells (reviewed in [41]). Histone modifications, DNA methylation, and other chromatin remodeling mechanisms, including deposition of histone variants and ATP-dependent chromatin remodelers, also seem to serve as a memory for priming in plant immunity [42], [43]. In some cases, acquired immunity can be passed from mother to offspring, endowing the offspring with improved defense against infection (transgenerational immune priming). For instance, a very recent paper has shown that in Arabidopsis thaliana, immune priming to Pseudomonas syringae is transmitted between plant generations through the hypomethylation of defense-related genes [44].

Future Directions

In this review, we have concentrated our attention on the current evidence available for the role of epigenetic mechanisms in pathogens' life cycle and pathogen-induced modification of host phenotype. However, epigenetics not only represents a paradigm shift in our understanding of host and pathogen phenotypic plasticity. We believe that in the next few years, perhaps the most exciting developments in the field of epigenetics will come by linking epigenetic variation and inheritance to the epidemiology and evolution of infectious diseases.

Epigenetic epidemiology has recently emerged as a promising area for future research on infectious diseases [29], [45]. In recent years, disease association studies based on epigenomic mapping have arisen as a powerful tool for disease risk prediction in humans. But these studies typically face the “chicken-and-egg” causality problem: there is an association between a particular disease phenotype and the epigenome, but it is not easy to establish whether it is the disease which is causing the epigenetic changes or whether the epigenetic changes are the ones causing the disease pathogenesis [29]. New epidemiological approaches are, however, being developed in epigenetic disease studies to control for such cause–effect relationships [46]. However, the reversible and context-dependent nature of epigenetic changes poses serious caveats to epidemiological studies. For example, many epigenetic changes linked to disease risk can be lost after one generation, change from tissue to tissue, or be differentially expressed in an age-dependent, sex-, and parent-of-origin-specific manner [47]–[49]. To overcome these difficulties, epigenetic studies of disease must be accompanied by comprehensive longitudinal (multistage and multi-individual) and transgenerational data. Although there is a lot of effort to bring epigenetics into epidemiological research in several noninfectious human diseases (see examples reviewed by [50], [51]), we still know very little about the consequences of epigenetic processes in the emergence and epidemiology of infectious diseases. Therefore, a comprehensive survey of epigenetic determinants of pathogenesis coupled with population-level epigenetic diversity studies in host–pathogen systems is needed before any disease prediction and prevention strategies can become a reality [52].

The second area of research is the role of epigenetic variation in host and pathogen coevolution and evolution. Since the incorporation of epigenetic inheritance and epigenetic plasticity mechanisms to evolutionary models and empirical studies of host–pathogen interactions is still lacking, our discussion is necessarily speculative. However, we envisage several areas that are ripe for future research. Models of host–pathogen co-evolution assume the presence of genetic variation for host resistance and pathogen infectivity, as well as genotype-specific interactions [53]. Mechanisms of genetic variation alone are, however, often unsatisfactory to explain the compatibility between host and pathogen phenotypes [54], and nongenetic inheritance mechanisms may have an important role to play (e.g., [55]–[57]). In addition, host–pathogen co-evolutionary interactions are often context-dependent (i.e., spatially and temporally variable), and the output of infection often depends upon several environmental factors such as temperature or nutrition [58]. Given the prominent role of epigenetic processes in environmentally induced phenotypic plasticity and adaptation [59], the fact that genotype-by-environment interactions in host–pathogen systems are epigenetically regulated seems a reasonable assumption. The work by Laine et al. [60] on a fungal pathogen and its host plant has, for example, demonstrated a temperature-dependent effect on pathogen performance on local versus foreign hosts. Multiple cases of environmentally triggered co-adaptations have been reported in several other host–pathogen systems (reviewed by [61]), which we contend will provide the raw material for future epigenetic studies.

A further unresolved matter is to establish the extent, nature, and significance of epigenetic inheritance in host–pathogen interactions. For example, transgenerational immune priming in invertebrates [62]–[64] and plants [42] is likely to have an epigenetic component, but the actual mechanism of inheritance is not known. Other transgenerational infection effects on host behavior and physiology, often so-called maternal effects, still need to be investigated (reviewed by [13]). Several authors (Bonduariansky and Day [9], Bossdorf et al. [65], Ho and Burggren [66]) have provided recommendations for testing epigenetic inheritance experimentally, which could be cross-applied to host–pathogen studies (Figure S1). In addition, there is an urgent need for epigenetic studies to develop solid theoretical evolutionary models [67]. Bonduriansky and Day [9] have suggested that epigenetic inheritance allows us to overcome three major limitations of genetic inheritance on phenotypic evolution: (1) It allows for traits acquired during the lifetime of an individual to be directly transmitted to the offspring, (2) it allows the transmission of favorable trait combinations across generations (genetic recombination tends to break such combinations), and (3) it provides an additional source of phenotypic variation for selection to act upon. At present, however, we know startlingly little about how these phenomena may impact the evolution of host–pathogen interactions. In this sense, the collaboration between molecular epigeneticists, functional and experimental parasitologists, and theoretical evolutionary biologists is needed to extend the current gene-based view of host–pathogen interactions into a more integrated one that includes both genetic and epigenetic dimensions.

Concluding Remarks

In recent years there has been an explosion in the number of epigenetics papers across biological disciplines (Figure 2), a progression that has been accompanied by technological breakthroughs that now make it possible to undertake sophisticated epigenomic studies across a range of organisms (Box 2 and Table S1). However, studies on the complex and multifaceted co-evolutionary interactions between hosts and pathogens have received comparatively little attention (Figure 2), and this in spite of their potentially evolutionary and epidemiological implications.

In this review, we have concentrated our attention on the current evidence available for those few cases in which an epigenetic mechanism has been described (i.e., see Table 1), but we lack evidence on the evolutionary and epidemiological significance of these changes. Conversely, there are many pathogen and host traits of key epidemiological importance that may be epigenetically controlled, some of which may have transgenerational consequences and whose mechanistic basis would merit further investigation.

In conclusion, the future is bright for the epigenetics of host–pathogen interactions. We are confident that in the next few years, cutting-edge epigenomic techniques combined with experimental (whole organism), functional, and theoretical (modeling) approaches will provide fascinating insights into the interrelations between genetic, epigenetic, and phenotypic variation in the complex world of host–pathogen relationships (Figure S2).

Supporting Information

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