MicroRNAs in the regulation of immune response against infections

Abstract

Innate immunity is considered to provide the initial defense against infections by viruses, bacteria, fungi, and protozoa. Detection of the signature molecules of invading pathogens by front-line defense cells via various germline-encoded pattern recognition receptors (PRRs) is needed to activate intracellular signaling cascades that lead to transcriptional expression of inflammatory mediators to coordinate the elimination of pathogens and infected cells. To maintain a fine balance between protective immunity and inflammatory pathology upon infection, the innate signaling pathways in the host need to be tightly regulated. MicroRNAs (miRNAs), a new class of small non-coding RNAs, have been recently shown to be potent modulators that function at post-transcriptional levels. Accumulating evidence demonstrates that the involvement of microorganism-encoded and host miRNAs might play instructive roles in the immune response upon infection. Here, we discuss the current knowledge of miRNAs in the regulation of immune response against infections.

1. Introduction

MicroRNAs (miRNAs) are a class of 19 to 24 nucleotides (nt) noncoding RNAs transcribed from the genomes of all multicellular organisms and some viruses. During this decade, there has been a tremendous increase in the number of miRNAs discovered in organisms (O′Neill et al., 2011). Their roles have been described in development, defense, and apoptosis. More than 30% of protein-coding genes are thought to be regulated by miRNAs at the post transcriptional and translational levels. miRNAs are initially transcribed by RNA polymerase II in the nucleus as primary miRNAs (pri-miRNAs). The pri-miRNA may contain one or several stem-loop structures that are cleaved by the nuclear RNaseIII type enzyme Drosha to produce a short hairpin precursor miRNA (pre-miRNA) transcript which can be shuttled into the cytoplasm. Pre-miRNA is finally matured by Dicer in the cytoplasm into the functional 22-base-pair (bp) double-stranded RNA (dsRNA), which is incorporated into the RNA-induced silencing complex (RISC) and forms the mature miRNA. Recent findings have shown that the majority of miRNA binding sites are in the 3′ untranslated region (3′ UTR) of target mRNA molecules and target interaction results in the degradation of the mRNA or translation repression (Alam and O′Neill, 2011).

Upon infection, sentinel cells such as neutrophils, macrophages, and dendritic cells (DCs), detect various invading pathogens through germline-encoded pattern recognition receptors (PRRs), which sense invariant microbial components termed pathogen-associated molecular patterns (PAMPs) derived from viruses, bacteria, fungi, and parasitic-protozoa (Takeuchi and Akira, 2010). Toll-like receptors (TLRs) represent the most studied PRRs and multiple aspects of the immune response have been shown to be controlled by TLRs. Besides TLRs, many other PRR families have been described, including retinoic acid-inducible gene (RIG)-I-like receptors (RLRs), Nod-like receptors (NLRs), and C-type lectin receptors (CLRs) (Desmet and Ishii, 2012; Hardison and Brown, 2012). PRR signals elicit signaling cascades, including those mediated by mitogen-activated protein kinases (MAPKs), nuclear factor-κB (NF-κB), and interferon regulatory factors (IRFs), which lead to up-regulation of type I interferons and proinflammatory cytokines that orchestrate innate and adaptive immunities to infection. Some NLRs assemble in inflammasomes, which control the activation of the cysteine protease caspase-1, and subsequent processing of interleukin (IL)-1β and IL-18 (Rathinam et al., 2012). However, PRR activation is a double-edged sword, as it is essential for provoking the innate response and enhancing adaptive immunity against pathogens, while inappropriate activation can also result in pathological inflammation as well as diseases. There is growing evidence to indicate that PRR signaling and functions need to be tightly regulated and many molecules have been identified as positive or negative regulators of immune response against infections (Qian and Cao, 2012).

Recent reports also throw light into the role of miRNAs as critical effectors in the regulation of host-pathogen interaction networks (O′Connell et al., 2012). The involvement of some miRNAs might be a part of a host response to an infection to dissemination of the microorganism or limit replication. Interestingly, the host miRNA pathway could also be manipulated by the microorganism to facilitate its replication. Understanding how the immune response is regulated by miRNAs during infection will obviously facilitate the development of new strategies to control PRR-mediated inflammatory diseases. In this paper, we comprehensively review the recent progress in the field of the regulation of immune response against infections by miRNAs.

2. miRNAs in the regulation of immune response against viral infection

RLRs and TLRs are the two major receptor systems employed by the host for detecting RNA virus infection and evoking antiviral responses by producing type I interferons (IFNs). Many positive or negative regulators of this process, such as neuregulin receptor degradation protein 1 (Nrdp1) (Wang et al., 2009), constitutive heat shock cognate 70 (HSC70)-interacting protein (CHIP) (Yang et al., 2011), SH2-containing protein tyrosine phosphatase 1 (SHP-1) (An et al., 2008)/SHP-2 (An et al., 2006), and β-catenin (Yang et al., 2010), have been characterized. Recently, miRNAs have emerged to be involved in the host immunity to virus invasion, or in virus infection to create favorable intracellular environments for virus replication (Skalsky and Cullen, 2010).

Some viral miRNAs have been discovered recently to regulate viral gene expression through degradation of viral transcripts. For example, Epstein-Barr virus (EBV)-encoded miRNA miR-BART2 guides cleavage within the 3′ UTR of the viral DNA polymerase BALF5 by virtue of its complete complementarity to its target, which is compatible with the notion that EBV-miR-BART2 inhibits transition from latent to lytic viral replication (Barth et al., 2008).

Recent reports suggest that some viral miRNAs regulate host gene expression by engaging in novel regulatory relationships or by mimicking cellular miRNAs, and thereby utilizing predefined cellular regulatory networks. It has been recently reported that human cytomegalovirus (HCMV) can use a virus-coded miRNA miR-112-1-mediated suppression of the viral immediate-early protein 1 mRNA as part of its strategy to enter and maintain latency (Murphy et al., 2008). miR-K12-11 miRNA encoded by Kaposi’s sarcoma-associated herpes virus (KSHV) is an ortholog of cellular miR-155 and is probably evolved to exploit a pre-existing gene regulatory pathway in B cells, contributing to the induction of B-cell tumours in infected patients (Gottwein et al., 2007).

Conversely, cellular miRNAs can also affect viral replication and pathogenesis, strikingly exemplified by the fact that host miR-122 facilitates hepatitis C virus (HCV) replication (Randall et al., 2007). Moreover, Triboulet et al. (2007) have recently found that human immunodeficiency virus type 1 (HIV-1) infection actively suppresses the expression of cellular miR-17/92 that represses viral replication via the histone acetyltransferase Tat cofactor p300/CBP-associated factor (PCAF). Infection of vesicular stomatitis virus (VSV) in macrophages induces miR-146a expression in an RIG-I dependent manner, and then miR-146a suppresses VSV-triggered type I IFN production by targeting IL-1 receptor-associated kinase 1 (IRAK1), IRAK2, and tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) so as to promote VSV replication (Hou et al., 2009). By targeting p300, miR-132 has been shown to be highly up-regulated after herpes simplex virus-1 (HSV-1), KSHV, or HCMV infection, and has a negative effect on the expression of IFN-stimulated genes, facilitating viral replication (Lagos et al., 2010).

There is mounting evidence that the production of type I IFN is critical for the antimicrobial response. Recently, it has also been shown that miR-466l can directly bind to the 3′ UTR of IFN-α and reduce its expression during VSV infection (Li et al., 2012). Type I IFN is also involved in the manipulation of miRNA expression. For example, IFN-α activation has been shown to suppress miR-378 and miR-30e expression to release cytolytic molecule mRNAs for their protein translation and then augment natural killer (NK) cell cytotoxicity (Wang P. et al., 2012). Induction of miR-155 by VSV infection has been shown to suppress suppressor of cytokine signaling 1 (SOCS1) expression in macrophages and subsequently enhance type I IFN effector gene expression and type I IFN-mediated antiviral response, thus suppressing viral replication (Wang et al., 2010).

3. miRNAs in the regulation of immune response against bacterial infection

The realization that TLR sensing of bacterial components contributes to the onset of many clinical features of sepsis reinforces the interest of immunologists in PRRs. TLR signalling can be broadly divided into two pathways: the myeloid differentiation primary response gene (88) (MyD88)-dependent and Toll/IL-1 receptor domain-containing adaptor inducing IFN-β (TRIF)-dependent pathways (Netea et al., 2012). Many factors have been identified as being essential for full activation of TLR responses, such as major histocompatibility complex class II (MHCII) (Liu et al., 2011), CMRF-35-like molecule 3 (CLM-3) (Wu et al., 2011), heat shock protein 70 (HSP70) (Chen et al., 2009)/HSP70L1 (Fang et al., 2011), and nerve growth factor (NGF) (Jiang et al., 2007). There is also evidence that many molecules can negatively regulate TLR signaling, such as Src homology 2 domain-containing inositol-5-phosphatase 1 (SHIP1) (An et al., 2005), protein-tyrosine phosphatase 1B (PTP1B) (Xu et al., 2008), cluster of differentiation molecule 11b (CD11b) (Han et al., 2010), platelet endothelial cell adhesion molecule 1 (PECAM-1) (Rui et al., 2007), Rab7b (Wang et al., 2007; Yao et al., 2009), and MHCI (Xu et al., 2012). Several miRNAs are induced by TLR activation in innate immune cells and have emerged as important controllers of TLR signalling.

Multiple miRNAs are induced in innate immune cells, with a consensus emerging that miR-155, miR-146, and miR-223 are particularly up-regulated and target TLR signalling proteins during bacterical infection. miR-155 has been demonstrated to increase during maturation of human monocyte-derived DCs after exposure to lipopolysaccharides (LPS) and directly target PU.1 mRNA (Hu et al., 2010). Upon Helicobacter pylori infection, the induced miR-155 has also been identified to target MyD88 (Tang et al., 2010). In human monocyte-derived DCs, miR-155 is identified to target transforming growth factor β-activated kinase 1-binding protein 2 (TAB2), a signal molecule downstream of TRAF6 which activates MAPK kinases (Ceppi et al., 2009). Inhibition of miR-155 leads to elevated activation of p38 pathway. miR-155 can also directly target the transcription factor Foxp3 (Kohlhaas et al., 2009). Exposure of cultured macrophages and mice to LPS could lead to up-regulation of miR-155 and that the transcription factor c/ebp β is a direct target of miR-155 during inflammatory responses (Worm et al., 2009). In addition, miR-155 could directly target several molecules involved in TLR4 signaling, such as the Fas-associated death domain protein (FADD), IκB kinase ε (IKKε), and the receptor (TNF receptor (TNFR) superfamily)-interacting serine-threonine kinase 1 (Ripk1) while enhancing TNF-α translation (Tili et al., 2007). miR-146a was found to repress two key adapter molecules downstream of TLRs: IRAK1 and TRAF6 (Taganov et al., 2006). TLR9-triggered miR-146a up-regulation has also been identified to target Notch1 in DCs, which is responsible for the reduced IL-12p70 production, subsequently promoting DC cross-priming of the cytotoxic T-lymphocyte (CTL) response (Bai et al., 2012). Recently, IRAK2 has also been confirmed as a target of miR-146 (Wang L.L. et al., 2012). miR-223 has been found to be dramatically decreased during human monocyte-macrophage differentiation, leading to increased expression of the serine-threonine kinase IKKα in macrophages (Li et al., 2010). Recently, Chen et al. (2012) demonstrated that inducible miRNA-223 down-regulation promotes TLR-triggered IL-6 and IL-1β production in macrophages by targeting STAT3. Inhibiting the activity of miR-223 has also been shown to decrease LPS-induced IFN-γ in splenic lymphocytes from estrogen-treated mice (Dai et al., 2008).

Many other miRNAs have also been demonstrated to target certain components of the TLR signalling pathway by certain miRNAs. miRNA-148/152 can regulate the innate response and antigen presentation of TLR-triggered DCs by targeting CaMKIIα (Liu et al., 2008; 2010). More recently, miR-466l has been shown to up-regulate IL-10 expression of both mRNA and protein levels in TLR-triggered macrophages by antagonizing the RNA-binding protein tristetraprolin mediated IL-10 mRNA degradation (Ma et al., 2010). Ma et al. (2011) found that infection of mice with Listeria monocytogenes or Mycobacterium bovis bacillus Calmette-Guérin (BCG) down-regulated miR-29 expression which subsequently suppressed immune responses by directly targeting IFN-γ.

4. miRNAs in the regulation of immune response against parasite infection

Evidence is accumulating that the miRNAs are implicated in the course and outcome of parasite infection. miR-27b has recently been shown to target KH-type splicing regulatory protein (KSRP) and modulate inducible nitric oxide synthase (iNOS) mRNA stability, a process that may be relevant to the regulation of anti-microbial defense from epithelial cells infected with Cryptosporidium, a protozoan parasite that infects the gastrointestinal epithelium and causes a diarrheal disease (Zhou et al., 2012). In addition, human miR-17 family members have been found to increase upon infection with the intracellular parasite Toxoplasma gondii, while the detailed information about the direct intervention of parasites in the alteration of host miRNA levels and how this is regulated by parasites at molecular levels is still lacking (Zeiner and Boothroyd, 2010).

5. Conclusions

miRNAs are “fine-tuners” of the immune response against multiple infections. Both pathogenic specific miRNA sequences and the phenomenon of the alteration of host miRNA levels after infection are known and further added a new layer of complexity to the area of post-transcriptional regulation in the area of innate immunity. Because of the ability of miRNAs to function as key regulators of the gene expression, it is not surprising that aberrant miRNA expression has been implicated in several infectious diseases, providing the prospective uses of miRNAs as clinical non-invasive biomarkers. Furthermore, the possibility for a relatively easy manipulation of the miRNA machinery and the apparent lack of adverse events when administered place miRNAs as promising targets for the treatment of infections.