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[Full text] The Risks of miRNA Therapeutics: In a Drug Target Perspective

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Introduction

In 1993, Lee et al discovered endogenous single-stranded approximately 22-nt lin-4 (a miRNA) could decrease the level of LIN-14 protein in C. elegans,1 and since then, researchers have reported a series of miRNAs that could inhibit the expression of specific proteins. In 2001, Elbashir et al reported double-stranded 21-nucleotide (nt) siRNA could induce RNA interference (RNAi) in different mammalian cell lines,2 and soon siRNAs were used as useful tools for gene silencing in biomedical research. Both types of RNA molecules could lead to inhibition of gene expression, but miRNA is complementary to the 3ʹ untranslated region of mRNA1 and siRNA is complementary to the coding region of mRNA.2 However, two similar mechanistic RNA molecules were under different progression for biomedical applications. In 2006, Craig Mello and Andrew Fire were awarded the Nobel Prize in Physiology or Medicine for their contributions to RNAi, which, however, excluded work on miRNA. Until 2020, a number of treatments based on siRNA technology have undergone  clinical trials, and two such products, patisiran3 and givosiran4, have been approved. But nearly 30 years later, miRNA did not benefit treatment of diseases even with none entering phase III clinical trials. In this article, we explore the delayed development of miRNA in a drug target perspective, and identify therapeutic risks of miRNA despite its great appreciation by many reports.5–9

Comparison of miRNA Drugs and siRNA Drugs

To understand the latest and detailed progression of RNAi, we first obtained clinical trial information of miRNA drug and siRNA drug (including shRNA, a small RNA molecule executing the same function as siRNA) from ClinicalTrials.gov,10 [email protected] database,11 a series of literature,3,4,12,13 and a company report14 (Tables 1 and 2). In our statistics, it launched 10 miRNA drugs in clinical trial, with one phase I, four phase II and five terminated/suspended (Table 1 and Figure 1A). However, 57 siRNA drugs (targeting human proteins/genes) were ongoing or completed clinical trials, including 16 phase I, 16 phase II, eight phase III, 23 terminated/suspended therapeutics (Table 2 and Figure 1A). As shown (Figure 1B), no miRNA drugs were in phase III trials, while siRNA drugs seemed to be in a complete clinical trial system without missing any segments. Moreover, we found that miRNA drugs suffered 50% terminated/suspended therapeutics, while 35.38% terminated/suspended therapeutics appeared in siRNA drugs (Figure 1B). Therefore, it may indicate there were potentially unclear obstacles for miRNA therapeutics.

Table 1 Clinical Information of miRNA Drugs

Table 2 Clinical Information of siRNA Drugs

Figure 1 Clinical progression of miRNA drug and siRNA drug. (A) The number of miRNA drugs and siRNA drugs in different clinical periods (terminated/suspended, phase I, phase II, phase III, approved). (B) The ratio of miRNA drugs and siRNA drugs of different clinical periods.

Inherently, miRNA is endogenously produced and siRNA is exogenously designed. Designers can exactly endow siRNA giving them the purpose of gene silencing, while endogenous miRNA seemed more complicated because nobody assigned them specific tasks. We mechanically analyzed the differences between miRNA and siRNA in their complementary modes with the target sequences. As expected, Figure 2A showed a flexible complementary ratio of miRNA with target sequence (within the range 20–90%) and none with complete complementation, but all siRNAs had 100% complementary ratio. The less restricted complementary mode may lead to low specificity of target sequence. Next, we employed miRTarBase15 to obtain targets of miRNAs for ten miRNA drugs, and compared the number of targets in miRNA drug* (referring to all targets of miRNA including experiment-validated and high-throughput results in miRTarBase), miRNA drug (referring to targets of miRNA only including experiment-validated results) and siRNA drugs. Beyond our expectation, the targets of the miRNA drug ranged from 30 to 250 in number and almost all miRNA drug* were over 500 and even 1000, but the si0052NA drug generally targets 1–3 genes (Figure 2B). The majority of miRNA targets tens and hundreds of genes, and we named it “too many targets for miRNA effect” (TMTME).

Figure 2 Flexible complementary ratio between miRNA with target sequence led to TMTME. (A) Complementary ratios of miRNA and siRNA with target. (B) Target number of miRNA drug* (all containing high-throughput results), miRNA drug (validated) and siRNA drug.

To further explore the cause for the delayed development of current miRNA therapeutics compared to siRNA drugs, we attempted to examine how many targets were not approved when these miRNA drugs entered into the tested subjects. Therefore, we collected all FDA-approved drugs (targeting human genes/proteins) from 1939 to 2019.3,4,16–19Figure 3A showed all ten miRNA drugs had tens and hundreds of unapproved targets, far beyond the siRNA drug. So, how many targets does a recognized drug have? We next profiled the target number of approved drugs (Figure 3B), and found the number of drug targets was no more than five. SiRNA drugs fell within the range, but miRNA drugs did not.

Figure 3 Target number of siRNA drugs obeyed the regular of all approved drug target number. (A) Unapproved targets of miRNA drug*, miRNA drug and siRNA drug. (B) Target number of miRNA drug*, miRNA drug, siRNA drug and approved drugs.

Analyses for Two Discontinued miRNA Therapeutics-based Projects

To further verify this finding, we collected and analyzed two available miRNA clinical projects that suffered discontinuation caused by adverse events. According to the ClinialTrials.gov database10 (NCT01829971) recorded, MRX34 (a miR-34a mimic) in a phase I clinical trial led to tested objects undergoing five serious immune-related adverse events, therefore terminating the project. Using KOBAS (a web server for annotation and identification of enriched pathways and diseases),20 we enriched 139 experiment-validated target genes of miR-34a in pathway analysis, and selected the top ten pathways, see Figure 4A according to the ranking of enrichment score and Figure 4B according to the ranking of number of genes. It showed that two immune-related pathways (cytokine signaling in the immune system and immune system) were on the list, and some related pathways like signaling by interleukins were also included. We further found that there were 15 approved genes and 25 unapproved genes in the immune system pathway and 13 approved genes and 16 unapproved genes in cytokine signaling in the immune system pathway (Figure 4C). Based on these facts, it is not hard to understand the emergence of five serious immune-related adverse events in phase I. According to the literature12 and the Regulus Therapeutics Inc. company report,14 RG-101, an anti-miR-122 drug, succeeded in phase I but was discontinued in phase II for the occurrence of a few cases of hyperbilirubinemia. We next enriched 71 experiment-validated target genes of miR-122 in disease analysis by KOBAS web server. However, no hyperbilirubinemia-related diseases were among the listed top 10 (Figure 4D and E). And hepatocellular carcinoma (HCC) was enriched as it has been reported that miR-122, a most frequent miRNA in the adult liver,21 played a crucial role in HCC in a series of literature,6,22,23 indicating the correctness of the enrichment. Given its emergence in phase II not in phase I, we filtrated 71 target genes in the literature and the KEGG database,24 and got seven hyperbilirubinemia or jaundice (hyperbilirubinemia-related disease) related genes (Figure 5). Only seven related genes were found, and it revealed why hyperbilirubinemia did not occur in most tested objects in phase I but appeared in a few cases in phase II.

Figure 4 Analyses of discontinuation of two miRNA-based clinical projects. (A and B) Enrichment for targets of MRX34 in terms of enrichment score and number of genes. (C) Unapproved and approved targets number of MRX34 validated targets in the immune system and cytokine signaling in the immune system. (D and E) Enrichment for targets of miR-122 (drug RG-101) in terms of enrichment score and number of genes.

Figure 5 Discontinuation of RG-101 is caused by its hyperbilirubinemia or jaundice-related targets. The hyperbilirubinemia or jaundice-related target genes of miR-122 are identified by literature searching and KEGG enrichment.

Future Directions and Conclusions

TMTME is a typical and inevitable property of miRNA molecules, which is caused by incomplete complementation with the target sequence. TMTME leads to that miRNA could bind to various sequences suitable for the interaction (including protein-coding genes, lncRNA,25 circRNA,26 etc), which is different from all approved drugs (including siRNA drugs) with only a few targets. Emerging siRNA-based products, patisiran and givosiran approved by the FDA, have been in clinical application, however, miRNA therapeutics was still in its early clinical stage. Therefore, both introduction and removal of miRNA in humans can lead to changes of a wide series of pathways and some of them are unknown, even unpredictable, probably triggering disorders of physiological function or the occurrence of additional disease.

Targeted drug delivery is a pattern of delivering drugs to specific lesion sites of a patient, largely based on nanomedicine, which can enhance solubility and efficacy of drugs and avoid needless interaction with healthy tissues.27,28 Targeted drug delivery systems can be designed by recognition of a specific feature in lesion sites.29 In cancers, the antigens and receptors on cell membranes are considered suitable targets of recognition sites for design of these nanoparticles.29 Therefore, targeted drug delivery systems may eliminate or weaken the existing obstacles that were caused by TMTME. Delivering miRNA drugs to pathogenic sites may efficiently avoid excessive toxicity and side effects. However, the defects of the system are high cost, hard to make productivity for delivering nucleotides, and the increased difficulty for adjusting the dosages.28,30 Moreover, due to instability of unprotected miRNAs, delivering miRNAs required chemical modifications to avoid rapid degradation in serum, which may impair specificity of miRNAs and lead to off-target effects.31 Besides, parenteral or local injection is the primary approach for delivering miRNA drugs,32 which reduces the amount of miRNA that is transported to the target tissue. Another challenge is that exogenous artificial miRNAs will trigger competition and saturation effect, a competition among exogenous and the endogenous miRNAs for the intracellular machinery, and thus affecting unexpected gene expression and leading to untoward side effects.33–35

Conclusively, in this study, we analyzed the key cause that leads to the slow development of miRNA therapeutics in a drug target perspective and attributed it to TMTME.

Resources, Databases and Servers

We use ClinicalTrials.gov database10 for obtaining available information of clinical trials, a series of literature36–89 for obtaining information for complementary ratio of miRNA with target gene, a study90 for getting all siRNA sequences with target genes, NCBI gene and NCBI blast database for calculating complementary ratio of siRNA with mRNA, KOBAS20 web server for enriching pathways and diseases for adverse events’ condition of miRNA therapeutics, KEGG database24 for obtaining hyperbilirubinemia or jaundice-related genes and pathways.

Acknowledgments

This work is supported by the National Natural Science Foundation of China (81902346) and Natural Science Foundation of Jiangxi Province (20192BAB215038).

Disclosure

The authors report no conflicts of interest in this work.

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