MicroRNAs (miRNAs) are endogenous oligoribonucleotides with exciting therapeutic potential. Early studies established a clear role for miRNAs in leukocyte biology. The first miRNA-based therapy, miravirsen, is now in phase 2 clinical trials, making the reality of these therapies undeniable. The capacity for miRNAs to fine-tune inflammatory signaling make them attractive treatment targets for immunological diseases. Nonetheless, the degree of redundancy among miRNAs, coupled with the promiscuity of miRNA binding sites in the transcriptome, require consideration when designing miRNA-directed interventions. Altered miRNA expression occurs across a range of inflammatory conditions, including inflammatory bowel disease, arthritis, and diabetes. However, very few studies successfully treated murine models of immunological diseases with miRNA-based approaches. While discussing recent studies targeting miRNAs to treat immunological conditions, we also reflect on the risks of miRNA targeting and showcase some newer delivery systems that may improve the pharmacological profile of this class of therapeutics.
MicroRNAs (miRNAs) are short (∼22 nt) untranslated single-stranded endogenous RNAs. They are transcribed either individually or as part of a polycistronic transcriptional unit, and the resulting primary miRNA transcripts are processed in the nucleus by the nuclear RNase III–like enzyme Drosha (1). The excised hairpin intermediates or precursor miRNAs are exported from the nucleus and processed into mature miRNAs by the cytoplasmic RNase III–like enzyme Dicer (2) (Fig. 1). The clustering of some miRNAs into transcriptional units suggests that they may have coevolved to perform redundant, complementary or sometimes antagonistic functions (3), a feature that is discussed later. Once formed, mature miRNAs are bound by argonaute (Ago) proteins and act as guide sequences that bind to short, 6–8-bp complementary motifs on target messenger RNAs (4), generally located within the 3′ untranslated region (UTR). The 6–8-bp complementary sequence at the 5′ end of the miRNA is called the seed. Perfect complementarity between the miRNA and its target triggers RNA interference, cleavage mediated by the RNase H–like domain of Ago2 (5, 6). However, in mammals, this has only been described for one target of miR-196 (7). In general, it is now believed that miRNAs promote deadenylation and mRNA decay at steady-state in somatic mammalian cells (8). Under specific circumstances, miRNAs were shown to inhibit initiation and/or elongation of protein translation (9). Recent evidence indicates that miRNAs repress protein translation by blocking assembly of the eukaryotic translation initiation factor, eukaryotic initiation factor (eIF)4F. Specifically, miRNAs form miRNA-induced silencing complexes with Ago proteins, which can either prevent association or actively displace the RNA helicase, eIF4A, from the eIF4F complex, thereby inhibiting the rate-limiting step in translation (10, 11). Regardless of the mechanism, posttranscriptional control of gene expression by miRNAs provides a molecular rheostat to modulate specific genetic circuits, offering an additional layer to fine-tune the degree of protein synthesis.
Current immunosuppressive therapies, such as steroids, induce broad-spectrum suppression of immune responses, which leads to increased susceptibility to infection. Targeting miRNAs may be of greater benefit for immunological diseases by limiting their action to a gentle nudge to restore the complex balance of our immune system between protecting and injuring the host. The feasibility of targeting miRNAs clinically has been given an enormous boost by the recent success of the pioneering miRNA-based therapeutic miravirsen (SPC-3649). A locked nucleic acid (LNA)-based inhibitor of miR-122, miravirsen is currently undergoing clinical trials for the treatment of hepatitis C viral infections (12). The role of the liver-specific miR-122 is somewhat unusual; instead of targeting the 3′ UTR and causing signal repression, it binds to the 5′ UTR of hepatitis C virus RNA and promotes its replication. Miravirsen’s success thus far paves the way for a new generation of miRNA-based therapeutics. Nevertheless, it must be noted that no approaches targeting miRNAs in the immune system have advanced to clinical trials. Effective targeting of hepatocytes by miravirsen does not guarantee the feasibility of targeting immune cells by any means. In fact, previous studies using unconjugated LNA-based miR-122 inhibitors demonstrated that significant accumulation of the LNA in hepatocytes occurred in an entirely passive manner upon i.v. injection (13). Therefore, as we shall discuss in greater detail, targeting of the immune system with miR-based therapeutics offers significantly greater challenges.
Indispensable role of miRNAs in immune cell development
Our understanding of the importance of miRNAs as a whole in immunocyte development and function initially came from genetically engineered mice carrying conditional mutant “floxed” alleles of the gene encoding Dicer, an enzyme critical for mature miRNA formation. Studies of T cell development demonstrate that early Dicer1 deletion in mice by the Lck-cre transgene impaired thymocyte proliferation and survival (14). Interestingly, restricting deletion of Dicer1 to a later stage of thymic maturation by using CD4-cre had significantly less impact on CD4+ T cell development (14). However, CD4-cre–dependent deletion of Dicer1 led to the development of colitis, as a result of a defect in T regulatory cells (Tregs) (15). Consistent with that concept, restricting Dicer1 deletion in CD4+ Foxp3+ cells resulted in the failure of Treg development, leading to lethal multiorgan autoimmunity, similar to that seen in the Foxp3-deficient scurfy mouse (16, 17). Therefore, although mature miRNAs might be partially dispensable for effector CD4+ T cell function, they are critical for the development of Tregs. Deletion of Dicer1 in CD8+ T cells results in more rapid T cell activation and impaired tissue egress (18), with both CD4 and CD8 T cell subsets displaying increased susceptibility to apoptosis (19). Furthermore, in the absence of Dicer, IFN-γ is aberrantly expressed upon Th2 cell differentiation, suggesting that miRNAs are essential for regulating Th2 cell plasticity. A similar phenomenon was observed in vivo during viral infection (20), and miRNAs may provide one molecular mechanism that can control cell fate and ultimately shape immune responses. Cell-specific Dicer1 deletion also identified important roles for miRNAs in the development and differentiation of B cells (21, 22), dendritic cells (23), and mast cells (24).
Although these studies attest to the critical role of miRNAs in the maturation of the murine immune system, the global nature of the intervention—stopping production of all mature miRNA—makes it difficult to determine whether a single miRNA (or many miRNAs) may be responsible for the resulting phenotypes. Although there are miRNA target prediction algorithms, such as TargetScan (4) and PicTar (25), it is essential for the field to be able to identify and validate direct miRNA targets experimentally in a high-throughput fashion. Invaluable protocols, such as photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation, although it requires metabolic labeling, and high-throughput sequencing after UV–cross-linking and immunoprecipitation, which suffers from high background, have been developed (26, 27) for target identification. However, a good Ab or affinity tag to enrich for Ago protein and large numbers of cells are required for these approaches, which can limit the feasibility of experimental designs. For cross-linking and immunoprecipitation, it is essential to have a negative control, such as an miRNA-deficient control, to help to determine which Ago-binding events are miRNA dependent (28). Moreover, the field needs a better way to validate miRNA targets rather than highly artificial luciferase reporter constructs in a heterologous transformed cell line. Although, it would be burdensome to mutate endogenous miRNA binding sites, perhaps the field could propose agreeable alternate solutions.
Nonetheless, the importance of miRNAs in immune cell development makes them exciting targets for novel diagnostics and therapeutic development. Later in this article, we discuss a number of the more critical hurdles associated with the successful targeting of specific miRNAs for therapeutic intervention. However, we first discuss examples in which targeting of a specific miRNA has a beneficial effect on immunopathology.
Therapeutic targeting of miRNAs for the treatment of immune diseases
Ongoing research has progressed to the elucidation of specific miRNA actions. For example, one of the first studies demonstrated that miR-155 is required for germinal center reaction upon immunization (29, 30). Deletion of miR-155 curbed autoimmunity in a mouse model of lupus (31). Subsequently, it was shown that Th17 cells require miR-155 for development, and deletion of miR-155 confers resistance to experimental autoimmune encephalomyelitis (EAE) and uveitis (32–34). Similarly, miR-155 was proposed as a potential therapeutic target for arthritis (35, 36). This body of work has been invaluable in furthering our understanding of how an individual miRNA contributes to the regulation of disease mechanisms. It also alerts us to the possibility that mutations in miRNAs or targets thereof (3′ UTRs) result in human genetic disease. Certainly, miR-155 loss-of-function mutations in humans would be predicted to cause immunodeficiency.
An exciting proof of principle has come from studies in which miRNAs were successfully targeted using synthetic miRNA inhibitors (33). One type, called antagomirs, are antisense 2′-O-methyl-modified, phosphorothioate-linked oligo-ribonucleotides conjugated to cholesterol that are designed to enter cells and anneal to the miRNA of interest (37). However, these must be used with caution because they recently were identified as potent platelet activators (38). Intranasal administration of miR-126 or miR-145 antagomirs in mice inhibited Th2-mediated allergic airway disease induced by the house dust mite (39, 40). Separate studies demonstrated that this airway Th2 response is promoted by miR-106a and negatively regulated by let-7a (41, 42) and that modulation of the levels of these two miRNAs in mice attenuated lung inflammation, reduced airway hyperresponsiveness, and decreased Th2 cytokine IL-13 production. Recently, a study of miRNA expression in CD4+ T cells from lungs of asthmatic patients revealed elevation of miR-19a (43). The study further showed that miR-19 promotes the development of Th2 cells in mice and humans and suggest that inhibiting miR-19 might be useful for treating Th2-mediated immunopathology. However, it is important to understand the mechanism of action when targeting miRNAs to avoid unforeseen consequences. In many cases, the downstream targets of miRNAs have not been systematically determined in vivo.
An early example of successful inhibition of a single miRNA in a murine inflammatory model was directed against miR-326, an miRNA associated with Th17 fate determination (44). This study first demonstrated that miR-326 was significantly elevated in peripheral blood leukocytes of patients with multiple sclerosis. Lentiviral approaches were used to overexpress miR-326 and accelerate EAE onset or inhibit miR-326 and attenuate EAE development. It must be stressed that a lentiviral-based approach is not applicable to human disease. Although a number of clinical trials have been initiated using lentiviral approaches to treat immune disorders, including chronic granulomatous disease and Wiskott–Aldrich Syndrome, these have yet to reach phase 3 trial stage and are, by design, limited to in vitro transduction. It may be necessary to include cell-specific promoters in lentivector design to improve their selectivity. Subsequent studies demonstrated a role for miR-326 in the pathogenesis of diabetes mellitus, with a similar upregulation of miR-326 in PBLs from patients with ongoing islet inflammation (45). The role played by miR-326 across a range of diseases may have implications for investment in new therapeutics. Therapies applicable to multiple diseases offer increased patient population sizes, providing greater return on investment, and thereby making the cost of their research and development significantly more attractive. Traditional anti-inflammatories that proved beneficial for the treatment of one immunological disease have been successfully adopted for the treatment of others [e.g., anti–TNF-α Abs for rheumatoid arthritis (46) extended for use in Crohn’s disease (47)]. However, certain miRNA-based therapies may actually exacerbate other inflammatory conditions. For example, miR-20b, which is downregulated in multiple sclerosis and can be targeted for the treatment of EAE (48), is actually upregulated in ulcerative colitis and may represent a potential biomarker of disease (49).
Another consequence of targeting miR-326 is that it was shown to exert an oncogenic role in glioma patients (50). Therefore, chronic inhibition of miR-326 for the treatment of immunological diseases may come with an increased risk for oncogenesis. Thus, it will be important to generate miR-326–deficient mice and determine its functions in vivo to assess this risk.
Another miRNA, miR-10a, was shown to be protective in EAE (51). This study demonstrated that the combination of retinoic acid and TGF-β induced the expression of miR-10a in naive CD4+ T cells and that miR-10a overexpression in transferred CD4+ T cells limited disease onset. As with the previous study, this approach attenuated, but failed to completely abrogate, disease, consistent with the redundancy between miRNA regulatory pathways. It would be interesting to know whether the combination of miR-10a supplementation and miR-326 inhibition would yield an additive effect. Once again, increased expression of miR-10a must be approached with caution as it too promotes cancer cell growth, migration, and invasion (52).
Although a brief review of the literature might suggest that targeting anti-inflammatory miRNA would lead to increased oncogenesis, it may simply be an artifact of the cancer-heavy focus of miRNA research (at the time of writing, a PubMed search of “cancer” + “miRNA” yielded 15,563 entries, whereas “immune” + “miRNA” yielded 1,884 entries). Nevertheless, inadvertently increasing susceptibility to oncogenesis is already a feature of current anti-inflammatories, such as infliximab, the gold standard anti–TNF-α Ab for the treatment of inflammatory bowel disease (53). Moreover, a small increase may represent an acceptable risk, especially given the association between malignancy and unchecked chronic inflammation (54). This is not a new concern for immunosuppressive therapies (55), but it stresses the need to target miRNA with caution.
Importance of targeted delivery of miRNA-based therapies
As the aforementioned studies demonstrate, the risk for undesirable effects with miRNA targeting is significant. Successful approaches may depend on maximizing delivery to the target organ and, thereby, limiting off-target effects. Although systemic delivery might be adequate for a filtering organ, such as the liver, more localized delivery might improve positive outcomes in other tissues. The easiest way to restrict delivery might be to use traditional targeted-delivery approaches, such as rectal enema for the treatment of colitis (56) or topical delivery for dermatitis (57). In a similar way, it is not surprising that all of the successful miRNA therapeutic studies in lung inflammation models described previously involved intranasal administration of antagomirs (39–42) as a means of localizing delivery. In reality, however, even organ-specific delivery of miRNA-based therapeutics may often be unsuitable, as demonstrated by driving the expression of miR-141 to alleviate murine colitis (58). Despite the success of these studies, colonic delivery might be inappropriate in this situation because of the established association of miR-141 expression with colorectal cancer (59).
A small number of miRNAs provide their own solution to this issue via their intrinsic restriction of distribution. Site- or cell type–specific miRNAs, such as the endothelial-restricted miR-126 (60), or miR-935, whose expression is thought to be limited to eosinophils (61), are very much the exception rather than the rule. Even with cell type–specific expression of miRNA, their pleiotropic effects may make them unsuitable candidates for targeting. This has been best shown for miR-223 (62), a hematopoietic-specific miRNA that has a crucial function in control of myeloid lineage development. The multiple targets of miR-223 have caused controversy among rheumatology researchers who separately identified both beneficial and deleterious roles for miR-223 in arthritis (63).
The aforementioned studies highlight the need for suitable delivery mechanisms for new miRNA-based therapeutics, to be included as an integral part of any therapeutic design (Fig. 2). To that end, a number of novel platforms, mostly adapted from small interfering RNA–based or gene-delivery approaches, are being explored, such as stable nucleic acid lipid particles and short interfering ribonucleic neutrals specifically for targeting miRNAs (64, 65).
Difficulties associated with miRNA targeting
Redundancy: the capacity of multiple miRNAs to regulate expression of a protein.
Redundancy is thought to explain the failure of studies aimed at blocking miR-92a (66), an miRNA known to repress a number of proangiogenic factors, including integrin α5 (67). Although the study successfully demonstrated up to a 14-fold suppression of miR-92a in target organs in response to treatment, inhibition of miR-92a failed to have a proangiogenic effect (66), consistent with a possible redundant regulatory mechanism. There is significant redundancy within miRNA networks, such that it may be prudent to block paralogous miRNAs or, indeed, entire families of miRNAs, as demonstrated with miRNA sponges (68). These false substrates act as competitive inhibitors by mimicking 3′ UTRs and stably binding complementary miRNA. This allows the simultaneous inhibition of multiple miRNAs (69, 70).
Much like the therapeutic index of conventional therapies, understanding how much miRNA should be delivered/inhibited in a target cell is critical to the development of safe therapies. Overexpression of an miRNA can result in greater extraneous effects (71, 72) or have lethal consequences as the endogenous regulatory systems are overwhelmed (73). Thus, targeting of an miRNA must be done with a considerable degree of caution.
Inhibition of miRNA activity can be achieved using the antagonistic effect of synthetic RNAs that are complementary to the miRNA of interest, called antagomirs or aptamers. Naked delivery of miRNA antagomirs, aptamers, or LNAs (containing an additional bond between oxygen and carbon to improve stability) offers both benefits and disadvantages for the treatment of immune diseases. Unlike current therapies, such as anti–TNF-α Abs, which lose efficacy because of their capacity to elicit an Ab response (74), short nucleic acid sequences can be designed to avoid induction of an immune response to nonself RNA (75), making them significantly more attractive. Moreover, LNAs have considerably longer serum half-lives (76, 77) compared with current pharmacological or biological treatments. The downside of these approaches is the pleiotropic effects that may result.
These pitfalls have led to the development of encapsulation technologies that can be modified to selectively target specific tissues or cell types. The use of nanoparticles to selectively target immune cells is increasingly common (78). These approaches proved to be successful in the selective delivery of small interfering RNA for the treatment of immune diseases (79) and, therefore, offer considerable promise for future miRNA-based studies. Surface conjugation with targeting Abs may offer improved selectivity of the nanoparticles. One limitation of well-established liposomal delivery systems is that they are often charged nanoparticles that can have immunostimulatory effects as a result of their electrostatic interaction with cell surface molecules. Although cationic nanoparticles have long been known to induce proinflammatory signaling pathways and stimulate chemokine release (80, 81), this phenomenon is actually polarity independent because anionic nanoparticles can also augment immune responses. This side effect may actually produce a desirable additive effect in the treatment of immunological diseases, particularly those that benefit from additional Treg induction (82), such as mouse models of Crohn’s disease (83). Another technique that is gaining traction involves highjacking endogenous exosomes. This pre-existing miRNA delivery system offers some very exciting potential benefits.
Exosomal delivery of miRNA mimics
Although exosomes have been proposed as a novel means of miRNA delivery for therapeutic applications, this field is still very much in its infancy. Considerable strides are still necessary to fully understand the role(s) that exosomes play, if any, in miRNA trafficking under physiological conditions. Recent studies suggested that, during inflammatory conditions, CD4+ Tregs, which produce relatively large numbers of exosomes, deliver miRNA to other T cell subsets via exosomes in vivo as part of their suppressive function (84). This and other studies delivered miR-155 mimics using lymphocyte-derived artificially transduced exosomes because these are thought to express appropriate trafficking ligands on their surface (85). Exosome-like nanovesicles transfected with miR-150 and injected into recipient mice also were shown to suppress contact sensitivity dermatitis (86). Nonetheless, important concerns remain regarding the absolute numbers of miRNA molecules contained within exosomes in vivo and, hence, the potential for a functional role (87). As our understanding of exosome function expands (88), their potential therapeutic applications may also.
Although it is clear from the studies outlined above that there are still hurdles to the use of miRNA-targeting approaches for clinical applications, these challenges must be weighed against the possible benefits that targeting miRNAs may have. Moreover, the rapid expansion occurring in this field suggests that miRNA-based therapeutics that can dampen inappropriate immune responses, without the unwanted immunosuppression seen with current therapies, are close at hand. The main concerns to be considered when designing an miRNA-based approach include understanding the selectivity of the miRNA, redundancy of the miRNA, and specificity of the delivery approach. As long as researchers treat each of these issues as important components in the design process, the prospects of miRNAs as therapeutic targets remain promising.
We thank Joselyn N. Allen (Pennsylvania State University) for creating the scientific illustrations within this review. We also thank Kelley Brodsky, Sandra Hoegl, and Douglas Kominsky for helpful suggestions in writing this review. We apologize to those whose work could not be discussed because of space constraints.
This work is supported by the National Institutes of Health Intramural Research Program of the National Institute of Allergy and Infectious Diseases (to S.A.M.), National Institute of Diabetes and Digestive and Kidney Diseases Grant K01 DK099403-01 (to C.B.C.), and Crohn’s & Colitis Foundation of America Grant CDA 253596 (to C.B.C.).
Abbreviations used in this article:
experimental autoimmune encephalomyelitis
eukaryotic initiation factor
locked nucleic acid
regulatory T cell
The authors have no financial conflicts of interest.