Strategies to Modulate MicroRNA Functions for the Treatment of Cancer or Organ Injury

Abstract

Cancer and organ injury-such as that occurring in the perioperative period, including acute lung injury, myocardial infarction, and acute gut injury-are among the leading causes of death in the United States and impose a significant impact on quality of life. MicroRNAs (miRNAs) have been studied extensively during the last two decades for their role as regulators of gene expression, their translational application as diagnostic markers, and their potential as therapeutic targets for disease treatment. Despite promising preclinical outcomes implicating miRNA targets in disease treatment, only a few miRNAs have reached clinical trials. This likely relates to difficulties in the delivery of miRNA drugs to their targets to achieve efficient inhibition or overexpression. Therefore, understanding how to efficiently deliver miRNAs into diseased tissues and specific cell types in patients is critical. This review summarizes current knowledge on various approaches to deliver therapeutic miRNAs or miRNA inhibitors and highlights current progress in miRNA-based disease therapy that has reached clinical trials. Based on ongoing advances in miRNA delivery, we believe that additional therapeutic approaches to modulate miRNA function will soon enter routine medical treatment of human disease, particularly for cancer or perioperative organ injury. SIGNIFICANCE STATEMENT: MicroRNAs have been studied extensively during the last two decades in cancer and organ injury, including acute lung injury, myocardial infarction, and acute gut injury, for their regulation of gene expression, application as diagnostic markers, and therapeutic potentials. In this review, we specifically emphasize the pros and cons of different delivery approaches to modulate microRNAs, as well as the most recent exciting progress in the field of therapeutic targeting of microRNAs for disease treatment in patients.

Fig. 1.

Biogenesis of miRNAs is a multistep process (Lee et al., 2003, 2004; Calin and Croce, 2006; Ha and Kim, 2014; Bartel, 2018). miRNA host genes are located in intragenic or intergenic regions and are primarily transcribed into a long, capped (Bartel, 2009), and polyadenylated transcript (pri-miRNAs) by RNA polymerase II, which is often longer than several kilobases (Lee et al., 2004). The pri-miRNAs are first processed in the nucleus into a shorter hairpin-structured transcript (pre-miRNAs) by the nuclear enzyme Drosha (Lee et al., 2003). The hairpin-loop pre-miRNAs are exported into the cytoplasm through a nuclear member channel protein, Exportin-5 (Yi et al., 2003). In the cytoplasm, pre-miRNAs are further processed by Dicer to a hairpin-free duplex form of miRNA called mature miRNAs (Hutvágner et al., 2001; Ketting et al., 2001). The duplex miRNAs bind with Argonaute 2 (Ago2) and transactivation-responsive RNA-binding protein (TRBP) to form RISC, and then a functional strand of the duplex miRNA remains in RISC until it binds to its target mRNA while the unfunctional strand is degraded. The eight-base-long seed sequences on the mature miRNA recognize and bind to their partial complementary sequences on the 3′ UTR of target gene mRNAs. The complex between miRNA and mRNA rapidly represses the translation of mRNA into proteins and eventually leads to mRNA degradation (Bartel, 2009, 2018; Eichhorn et al., 2014). DGCR8, Drosha and DiGeorge syndrome chromosome region; ORF, open reading frame.

Fig. 2.

Functional orchestration to show how deregulated miRNAs can affect human cancers during malignant transformation, progression, invasion, and metastasis. Certain miRNAs are found to be downregulated in cancers, referred to as tumor-suppressive miRNAs (Calin et al., 2002, 2004a,b, 2005; Calin and Croce, 2006; Yanaihara et al., 2006). When those tumor-suppressive miRNAs, such as miR-15a/16-1 (Kasar et al., 2012), let-7 (Yu et al., 2007; Trang et al., 2010), miR-34a (Lodygin et al., 2008; Li et al., 2009, 2013a; Pang et al., 2010; Silber et al., 2012; Yamamura et al., 2012; Cosco et al., 2015; Gaur et al., 2015; Beg et al., 2017), and miR-29b (Huang et al., 2013; Wu et al., 2013; Xu et al., 2014), are reintroduced to the cancer cells, they induce cell cycle arrest, apoptosis, DNA damage response, and/or immune surveillance to inhibit cancer growth. On the other hand, some miRNAs, including miR-21 (Meng et al., 2007; Hatley et al., 2010; Ren et al., 2010; Gaur et al., 2011; Fabbri et al., 2012; Griveau et al., 2013; Pfeffer et al., 2015; Huo et al., 2017; Lee et al., 2017), miR-17-92 cluster (He et al., 2005; Sylvestre et al., 2007; Xiao et al., 2008; Olive et al., 2013), or miR-155 (Eis et al., 2005; Costinean et al., 2009; Wang et al., 2009; Fabani et al., 2010; Jurkovicova et al., 2014; Cheng et al., 2015), are often upregulated in cancer cells, referred to as onco-miRs, and they are responsible for cancer cell proliferation, angiogenesis, invasion, and metastasis. Therefore, the inhibition of active onco-miRs or suppression of onco-miR expression in cancer cells can also lead to cancer regression. The consequence of such miRNA deregulation is to reprogram the severe level of multiple cell signaling pathways enough to transform the fate of affected cells since single miRNA can repress the expression of multiple target genes. Development of a therapeutic approach based on targeting those deregulated miRNAs is expected to re-reprogram cellular function of cancer cells to execute suicide or sensitize to other conventional therapeutics by releasing target genes from the miRNA-based suppression.

Fig. 3.

Shuttling of miR-223 protects against acute lung injury. Infection or mechanical ventilation can result in acute lung injury, during which neutrophils will transmigrate through the vasculature to inflamed alveolae (Dengler et al., 2013). Recruited neutrophils release microvesicles containing miR-223, a microRNA highly expressed in myeloid lineage cells. MiR-223–containing microvesicles are shuttled to pulmonary alveolar type II cells, resulting in the transcriptional repression of its inflammatory target gene PARP-1. Inhibition of PARP-1 leads to the attenuation of pulmonary inflammation and tissue injury. Therapeutically, nanoparticle delivery of miR-223 to pulmonary epithelial cells could potentially dampen pulmonary inflammation to prevent and treat acute lung injury (Neudecker et al., 2017a,c).

Fig. 4.

MiR-223 in inflammatory monocytes dampens intestinal inflammation. DSS-induced intestinal injury leads to the upregulation of MiR-223 in inflammatory monocytes. Increased miR-223 levels result in the inhibition of its target gene NLRP3, and dampened NLRP3 sequesters inflammasome activity and downstream production of inflammatory cytokines, such as IL-1β. Turning down IL-1β attenuates intestinal inflammation and histologic signs of intestinal injury. Pharmacological enhancement of miR-223 could potentially alleviate acute gut injury and intestinal inflammation in the perioperative period (Neudecker et al., 2016, 2017b,c; Yuan et al., 2018a).

Fig. 5.

The mechanistic model of action in miRNA-based therapeutic modulation in the application for human diseases. Deregulated miRNA expression can be overcome either by the restoration of those downregulated tumor-suppressive miRNAs or inhibition of those upregulated onco-miRs in the diseased cells. Top: inhibition of upregulated miRNAs can be attained by the introduction of AMOs. Chemically modified nucleic acids LNA (Elayadi et al., 2002; Kurreck et al., 2002; Valoczi et al., 2004; Griveau et al., 2013; Di Martino et al., 2014) or PNA (Hanvey et al., 1992; Demidov et al., 1994; McMahon et al., 2002; Fabani et al., 2010) are used as single-stranded inhibitors. These are often further formulated into lipid or inorganic nanoparticles to protect them from serum degradation and/or enable a targeted delivery. Once internalized into the diseased cells, the complementary sequence of AMO recognizes and binds to its target onco-miR, of which double-stranded complex will be degraded and release the target gene mRNAs from the repression of protein synthesis by the onco-miR. Bottom: restoration of downregulated tumor-suppressive miRNAs in diseased cells can be achieved by the introduction of mimic sequences into the diseased cells. Viral vectors, such as (Jia et al., 2012; Kasar et al., 2012; Huo et al., 2017) or AAVs (Kota et al., 2009), are often used to induce overexpression of such downregulated miRNAs. Mimic miRNA sequences can also be delivered to the diseased cells in a formulation of liposomes (Rai et al., 2011; Campani et al., 2016; Beg et al., 2017; Xu et al., 2017) or inorganic nanoparticles (Kim et al., 2011; Sun et al., 2014; Ren et al., 2016; Xue et al., 2016; Setua et al., 2017) for protection from serum degradation.