Starting with the double-helical structure of DNA in 1953, the story of molecular biology has featured more characters than a Russian novel. Biologists have identified tens of thousands of molecules that direct and shape the organized chaos within the body's cells, and they have exploited those findings with thousands of drugs and treatments.
For decades the stars of the drama came from two camps: DNA, or deoxyribonucleic acid, which acts as a near permanent repository of genetic information, and proteins, which do the genes' handiwork. Protein discoveries have led to such medical advances as synthetic insulin, interferon and next-generation anticancer drugs. And gene therapy, using modified bits of DNA, has made headway against hemophilia, hereditary blindness and other previously intractable diseases.
Overlooked in this march of medical progress was a third type of biomolecule: RNA, or ribonucleic acid. Like its more famous sister, RNA contains genetic information, but it is less chemically stable than DNA and is often degraded by enzymes in the turbulent environment of the cytoplasm.
Although scientists have long known that RNA is intricately involved at some point in almost every cellular process, for most of the biomedical revolution they assigned it a supporting role, in the shadow of DNA and proteins. In the 1950s and 1960s biologists thought of RNA as a kind of Cinderella molecule, ferrying messages, coordinating supplies and generally keeping cells tidy. For decades this view stuck.
But that was before a few fairy godmothers (and godfathers) gave RNA a stunning makeover. A series of discoveries in the late 20th century revealed new forms of RNA that were nothing like humble housekeepers. On the contrary, these RNA molecules exerted an astonishing degree of control over the behavior of DNA and proteins—targeting specific molecules to increase or decrease their activity. By manipulating this RNA, scientists could potentially develop new treatments for cancer, infectious diseases and a wide range of chronic illnesses.
In the past decade or so investigators have raced to exploit this insight. The pace of discovery has accelerated, dozens of start-ups have formed to capitalize on new findings and now some promising treatments are in the offing.
Meanwhile an early trickle of financial interest has grown into a multibillion-dollar torrent. Among recent ventures, Editas Medicine received $43 million in venture capital for its launch at the end of 2013; the company is concentrating its efforts on the hottest new RNA technology, known as CRISPR. A slightly older company, Alnylam Pharmaceuticals, founded in 2002, received $700 million this past January to develop, among other things, its pipeline of RNA medications for devastating blood conditions, liver diseases and immune disorders.
The funding has come “in waves,” says Robert MacLeod, vice president of oncology and exploratory discovery at Isis Pharmaceuticals, which has raised nearly $3.8 billion since it was founded in 1989. Its lead product, Kynamro, received approval from the U.S. Food and Drug Administration in 2013 as an RNA medicine for people with a rare genetic disorder that significantly interferes with their ability to process cholesterol, putting them at an exceptionally high risk of heart attack and stroke.
As with any rapidly expanding field, there have been a few bumps and detours along the way, and not every discovery will likely stand the test of time. Yet medical researchers are practically giddy with excitement—as if they had found a new continent to explore in search of potential breakthroughs.Supporting Role
It is easy to see why molecular biologists would assign starring roles to DNA or proteins rather than RNA. DNA's main subunits—adenine, thymine, cytosine and guanine, or A, T, C and G—constitute the basic instruction manual for growing just about every living thing on the planet. And one of the most important processes that DNA provides directions (or codes) for is the creation of proteins.
Proteins, for their part, give cells their three-dimensional structure and allow them to perform many jobs; they provide the skin's youthful spring and the heart's lifelong strength. They also turn DNA on and off in response to environmental cues, determine how well cells use sugar and regulate the ability of neurons to relay signals to one another in the brain. The vast majority of today's medicines—from aspirin to Zoloft—work by manipulating proteins, either by blocking their function or by altering the amount that is produced.
Just because most medications affect proteins, however, does not mean that investigators have been able to develop drugs that act on all the proteins they would like to target. The most common pharmaceutical remedies consist of small molecules that can survive being swallowed and passed through the acidic interior of the stomach. Once absorbed from the digestive system, they must fit into the active locations on their target proteins the way a key fits a lock. But there are certain groups of proteins for which this traditional approach will not work. The proteins bury their active sites too far inside narrow channels, or they do not even contain an active site because they make up part of the cell's internal skeleton, which renders them “undruggable,” MacLeod says.
This roadblock is what the new RNA medicines are designed to overcome—though how they could do so has not been obvious until recently. As biologists have long known, RNA serves as a talented go-between, copying, or transcribing, DNA's instructions into a complementary sequence (matching a C for every G, for example) and then translating that code into three-dimensional proteins. So-called messenger RNA (mRNA), which is generated in the nucleus, travels to the cytoplasm, where structures called ribosomes and transfer RNA (tRNA) work together to read the message and connect amino acids (nitrogen-containing compounds) into long chains that become proteins. But RNA can do much more.A Star Is Born
The groundwork for RNA's breakout performance was laid in 1993, with the identification of the first microRNAs. These uncharacteristically short stretches of RNA attach themselves to strands of mRNA, preventing ribosomes from making any progress in assembling a protein [see box on preceding page]. Cells apparently use microRNAs to coordinate the production schedule of many proteins—particularly early in an organism's development. Five years later researchers made another breakthrough when they demonstrated that different short RNA molecules effectively silenced the translation of a gene into protein by cutting up mRNA. That landmark discovery later netted a Nobel Prize, in 2006.
By this point, everyone—not just RNA specialists—was seemingly interested in using the once overlooked molecule to influence how proteins were formed. The disruption of mRNA by short RNA molecules was coined RNAi, for RNA interference, and the latter molecules were given such names as siRNA, for small interfering RNA. Meanwhile a wide range of scientists realized that they might be able to deal with undruggable classes of proteins by moving the action further upstream, at the RNA level of the protein-manufacturing process.
To date, more than 200 experimental studies of either microRNAs or siRNAs have been registered through the U.S. government's database of clinical trials for the diagnosis or treatment of everything from autism to skin cancer. Among the most promising are treatments for Ebola virus, an extremely deadly pathogen that terrorism experts fear could be turned into a bioweapon, and hepatitis C, which has triggered long-lasting infections in about 150 million people around the world and is a major cause of liver cancer [see box at left and box on next page].What's Next?
Whereas medications containing microRNA or siRNA are furthest along in the race to the clinic, another generation of aspiring starlets is now waiting in the wings. These potential medications would work even further upstream, on the DNA molecule itself. One of the approaches is based on CRISPR sequences found in the DNA of many single-celled organisms and was enthusiastically described in Science as the “CRISPR Craze.” The other, which depends on the existence of molecules known as long noncoding RNAs, or lncRNAs, still faces some skepticism about its utility.
CRISPR stands for clustered regularly interspaced short palindromic repeats, which are oddly repetitive stretches of DNA found in bacteria and archaea (bacterialike organisms). These quirky sequences, in turn, interact with proteins known as CRISPR-associated, or Cas, proteins. Together CRISPR and various Cas proteins form a microbial defense system against viruses.
The proteins have one job—to cut DNA in two. They are guided to specific stretches of viral DNA by complementary strands of RNA. Where does the RNA come from? In a microscopic version of jujitsu, cells grab the RNA from the invading virus, turning it into a double agent that guides the Cas proteins to the exact spot where they need to cut.
Although CRISPR elements were first observed in bacteria in 1987, scientists started adapting the system to a wide range of animal, including human, tissue only in 2012. By creating their own guide strands of RNA, investigators could direct the Cas proteins to cut DNA molecules in the nucleus at very precise locations. In essence, they had turned the bacterial defense mechanism into a precision gene-editing tool.
Such exquisitely targeted technology could potentially revolutionize gene therapy—perhaps sooner rather than later.
Currently clinical investigators are only able to inject corrective DNA into patients with defective genes in a scattershot manner, hoping that at least some genetic material manages to start working in the right place. Fully developed CRISPR/Cas technology could change that by allowing researchers to choose precisely where a patient's DNA should be modified. “We're going to be seeing quite a few gene therapy trials using CRISPR in the next year,” says George M. Church, a professor of genetics at Harvard Medical School, co-founder of Editas and scientific adviser to Scientific American. “It basically works right out of the box,” he adds. “You can take it out of bacteria with minimal changes. Almost every guide RNA you'd want to make goes to a place that works. It's fast, and it's permanent.”
Church expects that Editas will proceed to clinical trials quickly after first completing animal studies. Other recently launched CRISPR-centric companies include Caribou Biosciences and Egenesis.
Finally, the most controversial of the latest RNA discoveries concerns lncRNAs. First described in 2002, these unusually lengthy stretches of RNA originate in the nucleus and look, at first glance, as though they might be mRNAs except that they lack certain sequences of letters required to initiate the translation process.
What could the cell possibly want with all these extra RNA molecules? Some of them undoubtedly result from the transcription of earlier versions of genes that are now broken and no longer functional. (One of the more surprising discoveries of the genetic revolution is that almost all DNA found in the nucleus is transcribed, not just the parts that code for proteins.) Others are probably echoes of long-ago attacks by certain kinds of viruses that can incorporate their genetic material into a cell's DNA, allowing it to be passed on through subsequent generations.
Yet what if some of the lncRNAs represent a previously unsuspected way of regulating the expression of genes—one that does not require potentially dangerous mutations in the DNA or that does not depend on proteins to play the starring role? Think of the DNA as being folded like origami, says RNA researcher John Rinn of Harvard University. With two identical pieces of paper, you could make a plane or a crane, and lncRNA somehow pushes the DNA to make sure the steps occur in the right order. Just as a mistake in origami folding could render the paper crane wingless, too much noncoding RNA, for example, might trigger the growth of a tumor without a single mutation ever having had to occur in the genes of the cell.
Another possibility under investigation is that lncRNA molecules may attach themselves to different parts of a DNA molecule, changing the latter's three-dimensional shape and therefore exposing it to, or hiding it from, further activity.
An entire host of other noncoding RNAs have been proposed and are in various stages of being confirmed as important genetic regulators or dismissed as genetic ghosts. One of the difficulties of studying noncoding RNAs is precisely the fact that they do not give rise to proteins—which makes it harder to prove that they are doing something important. “I think it's just the early days yet,” says John Mattick, a leader in research into noncoding RNA and director of the Garvan Institute of Medical Research in Australia. “There's a whole new world emerging here.”
Meanwhile considering the broad range of RNA compounds that are being designed and tested brings up what may be the molecule's most appealing feature—its simplicity. Unlike proteins, whose three-dimensional structure must typically be characterized before drug developers can create effective medications, RNA basically consists of a two-dimensional sequence (leaving aside, for the moment, some of the shapes into which RNA molecules can fold). “It's reducing a three-dimensional problem, where the small molecule has to fit perfectly into the protein in a lock-and-key-type fit, to a two-dimensional, linear problem,” Isis's MacLeod says. Thanks to the Human Genome Project, researchers already know the most important sequences in the genome. All they need to do is synthesize the complementary RNA strand, and they have created the bull's-eye for their efforts.
Figuring out how to put theory into practice is still a struggle, of course. But for now, at least, the magical glass slipper appears to fit.