MicroRNAs as Drugs and Drug Targets

MicroRNAs (miRNAs) play an important yet complicated role in regulating gene expression, and researchers are discovering ways to hijack this complexity to treat diseases, intervening with miRNA-based therapeutics. Changes in miRNA expression appear to play a role in a range of diseases, including many types of cancers, hepatitis, and Huntington disease. But the complex web representing a single miRNA’s mechanisms of action isn’t easily elucidated —or corrected, in the case of therapeutic interventions. For example, one miRNA can target multiple mRNAs, yet one mRNA might be influenced by multiple miRNAs. Furthermore, miRNAs can regulate each other. Such interconnectedness makes cause-and-effect relationships challenging to pinpoint in the lab, spurring the use of bioinformatics to zero in on likely miRNA candidates for drug targets. Then the challenges of delivering the miRNA-related drugs to the right places begin. This article looks at some of these challenges and recent developments in miRNA therapeutics.

Solving delivery challenges

Because one miRNA can regulate many mRNAs, it is a prime candidate (or target) for drugs to treat cancer or other complex diseases. Frank Slack, Director of the Harvard Medical School Initiative for RNA Medicine at Beth Israel Deaconess Medical Center, and colleagues have been leading efforts to deliver tumor suppressor miRNAs, and agents that target cancer-causing miRNAs, to particular types of cancer. The goal is to deliver, as a drug, either a miRNA, or an antisense oligonucleotide that targets a specific miRNA (known as an antagomir, or an anti-miR). “That’s been challenging because you have to get these fairly large molecules into the cancer cells,” says Slack.

Because miRNAs cannot cross cell membranes alone, researchers have developed ways to shuttle them into the cytoplasm where they act, by methods such as encapsulation in carrier liposomes, expression by viral vectors, addition of chemical modifications, or conjugation to biomolecules for receptor-mediated uptake. New tools such as aptamer conjugates also look promising in their ability to add targeting specificity to intracellular delivery. Aptamers are nucleic acids purposefully designed to bind to cell surface receptors with high affinity, and they can be annealed directly to a therapeutic miRNA for receptor-mediated delivery.

InteRNA Technologies developed a platform for the discovery of cancer-related miRNAs using non-biased phenotypic functional screening in cell-based assays, delivery with lipid nanoparticles, chemical modifications to encourage uptake in the RNA-induced silencing complex, and advanced bioinformatics to predict and validate candidate miRNAs. InteRNA Technologies’ CEO, Roel Schaapveld, notes that drug delivery has been their biggest challenge, “coming up with the right formulation that brings your cargo beyond the liver to tumor cells around the body.” After cellular uptake, a miRNA mimic finds its way to the RNA-induced silencing complex and binds to downstream RNAs. “Using changes in downstream mRNAs as a readout was for us the main criteria for effectiveness,” he says. “And it took us a lot of time to get there.” In addition to downstream transcriptomic analyses, they confirm the effectiveness of a miRNA therapeutic at the molecular and protein levels.

Delivering a tumor suppressor mimic

One of InteRNA Technologies’ miRNA drug candidates is a chemically modified mimic of a tumor suppressor miRNA, currently in Phase 1a trials for several types of cancers resistant to treatments with kinase inhibitors and chemotherapy, including liver cancer and triple-negative breast cancer. “Preclinically, we have also seen it attack other types of cancers, such as pancreatic cancer, melanoma, and colorectal cancer, and recently we got our first proof-of-principle that it can work in acute myeloid leukemia,” says Schaapveld.

This miRNA mimic, known as INT-1B3, changes the tumor microenvironment in ways that push tumor cells toward cell death, and influences pathways that tumor cells use to evade the immune system. “It was already known that if you can downregulate that pathway, you can increase the effectiveness of CTLA-4 and PD-1 inhibitors, and actually that is also what we see preclinically,” says Schaapveld. “Once we establish the right dose in Phase 1a, we’ll collaborate with a pharma company on a combination trial with an anti-PD1 antibody.”

Antagonizing an oncogenic miRNA

Inspired by recent targeting successes in the siRNA field, Slack and colleagues focused on delivery agents for miRNAs and antagomirs. “We’ve worked with organic chemists and biomedical engineers to make these molecules as drug-like as possible, and then encapsulate them in some sort of nanoparticle that helps us deliver them to the right place,” he says.

For example, the Slack lab is trying to deliver an antagomir to target an oncogenic miRNA in pancreatic cancer, an especially aggressive disease with no good drug treatment options. Pancreatic tumors are surrounded by fibrotic stroma, making drug delivery even trickier. “We teamed up with a biomedical engineer, Dr. Sangeeta Bhatia at MIT, who helped us design a nanoparticle that would allow us to deliver an antisense molecule into the tumors, to target the oncogenic miRNA,” says Slack, who continues to pursue targeting strategies for pancreatic tissue. “We haven’t got 100% success there, but we’re getting close, and we’re hopeful.”

Targeting and dosing

The Herculean efforts at target and delivery and engineering are necessary because so far, it’s the only way to deliver miRNAs to target cells at a concentration or dose that is low yet effective, without causing unwanted effects in other tissues. “Delivering these drugs at very high concentration will get them to the tissue that you want them to go to, but unfortunately, also to many other tissues, and that can be toxic,” says Slack. “So the key is a low dose targeted just to the right place.”

He is optimistic that the miRNA field will solve the targeting problem. The siRNA field discovered how to target drugs to the liver, for example, and he’s hopeful that the miRNA field will build on this to find delivery agents that target other tissues. “The field is definitely moving toward targeted delivery, either conjugating a chemical directly to the miRNA or the miRNA antagomir, or packaging these into some nanoparticle that can help you target it to the right place,” says Slack. Indeed, both fields are now searching for targeting moieties for delivery to many specific tissues.

In addition to delivery and targeting, other challenges facing the development of miRNA-based therapeutics include different administration methods (such as oral, inhalation, adoptive cell transfer, or implantation of 3D matrices that release therapeutics), stability after administration, and minimizing unwanted effects. With luck, the trend in miRNA therapeutics will continue to mirror that of siRNA therapeutics. “While we’ve been trailing the siRNA field, now miRNAs are showing some success,” says Schaapveld. “But the miRNA field needs some clinical success now, so that people start to see that this is a real therapeutic modality.”