Frank Bennett, Senior Vice President of Research, Isis Pharmaceuticals

Isis Pharmaceuticals, Inc., a world leader in developing technology to attack the genetic causes of diseases, is now engaged in the fight to stop Huntington’s disease.

Isis aims to block HD at its genetic root, and, if all goes as planned, it wants to test a drug in humans by late 2010.

On April 9 HDSA-San Diego visited Isis in Carlsbad, California, to meet the people who are seeking to relieve the suffering of tens of thousands of Huntington’s families and prevent the disease from destroying the brains of people who have tested positive for the disease but not yet shown its most obvious symptoms of shaking limbs and dementia.

A new technology

“We have a technology that prevents the huntingtin protein from being expressed,” said C. Frank Bennett, Ph.D., an Isis founder and its senior vice president of research. “If you don’t express the mutant form of huntingtin, you can abrogate or delay the onset of the disease.”

Isis developed that technology in a feasibility study carried out two years ago for Cure Huntington’s Disease Initiative, Inc. (CHDI), a Los Angeles-based non-profit foundation dedicated exclusively to finding a treatment or cure for HD. Isis demonstrated that it could block the action of the huntingtin gene in mouse and human cells and in actual mouse brains. All humans have huntingtin, but in some people it has gone awry, causing Huntington’s disease.

In October 2007 Isis and CHDI announced the current project, which seeks to control the mutant form of huntingtin. CHDI will provide Isis up to $9.9 million to carry out the various stages of the project. CHDI receives support primarily from an anonymous donor (the High Q Foundation) and is also supported by the Huntington’s Disease Society of America, and the Hereditary Disease Foundation.

The weapon: big molecules called ‘oligos’ and made like Tinkertoys

The technology is known as antisense. DNA, the building block of all life, runs our cells by telling them which proteins to make. It does so by sending messages with another molecule called messenger RNA. As encoded by DNA, RNA has a very specific template, somewhat akin to a unique electrical outlet into which only a unique plug can fit. RNA is known as a sense molecule, and Isis manufactures the antisense plugs to control them. These antisense molecules are called oligonucleotides, or oligos.

“Our technology allows one to basically, with a laser-guided missile, target that specific messenger RNA that causes a particular disease and kill it or take it out of the body so that you don’t produce that messenger RNA,” Dr. Bennett explained. “The result is that you prevent the bad protein from being expressed…. We’re designing oligonucleotides that will bind to the huntingtin messenger RNA, and upon binding to the messenger RNA, prevent it from being translated into a protein product.”

Dr. Bennett likened the manufacture of oligos to playing with Tinkertoys. Remember that Tinkertoys have circular pieces of wood with holes into which a child puts pencil-like sticks and thus builds a small structure. Isis does the same thing using a complex piece of machinery and produces extremely long molecules. “We do that with chemistry on a machine called an oligonucleotide synethisizer,” he said. Isis can make just a few grains of oligos for initial testing and then tons on much larger machines in order to test purity and prepare the oligos for commercial application in partnership with a larger pharmaceutical company.

Janet Leeds, Ph.D., CHDI’s director of pre-clinical development and the point person for the Isis project, used a similar analogy: “It’s kind of like knitting. You make one and then the other.”

Fine-tuning the approach

Using its unique chemical processes, Isis patents its oligo designs. In a field that once had other competitors, it is now the only company in the world working with its particular kind of antisense technology.

Isis’s strength lies in its ability to “measure RNAs in cells,” Dr. Bennet continued. Isis has a room with “rows and rows” of instruments for studying the RNA, “as well as robots that extract the RNAs from cells and put them on machines. We have really industrialized that part of the process.” According to Dr. Leeds, who spent eight years at Isis, the company has decreased the cost of producing oligos tenfold.

Isis is currently working on fine-tuning the oligo it developed in the feasibility study and has already tested over 200 compounds, said Dr. Leeds. Once the best match is found, it will test the oligo in transgenic mice provided by CHDI. Those mice are engineered with both a mutant human and mouse huntingtin gene. These mice were developed by Dr. William Yang of the University of California, Los Angeles. They develop Huntington’s-like symptoms. Isis employs a special clamp known as a stereotactic device to inject drugs into mice at exactly the same spot each time, and it uses other devices to measure the mice’s behavior, muscle strength and coordination, and brain function – all crucial factors in Huntington’s disease.

If mouse tests are successful, Isis will repeat the experiment in monkeys to make sure the oligo is safe for humans.

“We’re breaking ice in learning how to modulate huntingtin,” Dr. Bennett continued. “Nobody’s had a technology that would allow you to address what is the function of huntingtin in a developed organism. It clearly plays a role in normal physiology. It’s not well understand what that role is, but it seems to be important for some aspects of normal function of neurons as well as other cells in the body. It’s expressed everywhere in the body, not just in the brain.”

Making a safe drug

Now that Isis is close to an oligo, it faces two other huge challenges. First, because the oligo would regulate both normal and mutant huntingtin, Isis and CHDI must determine how much huntingtin should be controlled in order to reduce disease and avoid adverse effects. For now the plan is to reduce or “knock down” huntingtin’s action by about 50 percent, said Dr. Leeds.

“That’s no different than any other drug that we use today,” Dr. Bennett said. “Say if you take a use a drug that lowers your blood pressure. If you’re hypertensive, and are at risk for cardiac dysfunction, because you have high blood pressure, lowering your blood pressure is good. But you don’t want to lower it to zero! All drugs will produce toxicity if you overdose. The animal models will be very instructive for giving us that guidance, because we will be able to lower the normal level of huntingtin as well as mutant huntingtin and cover whatever are the potential adverse effects of that.”

Dr. Leeds added that the Isis scientists could end up discovering that each individual needs a particular molecule to regulate his or her level of huntingtin. But this “personal medicine” approach is not yet feasible.

Getting the remedy into the brain

Secondly, Isis must get the oligo into the brain.

CHDI is banking on Isis’s success in developing the world’s first antisense drug for the market, Vitravene, which is used to treat an eye disease associated with AIDS. Vitravene is injected directly into the eye. With current technology an oligo for Huntington’s disease cannot be delivered via a pill or injection into the brain, and any medication will have to cross the blood-brain barrier.

In the mouse experiment Isis inserted pumps under the animals’ skin and ran a tube into the brain. For humans a hockey puck-sized pump would go into the abdomen send fluid directly to the brain after a physician operated to insert the tube. He pointed out that people with a number of conditions such as chronic back pain or diabetes already use commercially approved pumps. Doctors can use infrared signals to program the pumps and control the flow of medication and can inject a new supply into a port just under the skin.

“It’s obviously not ideal, but considering the severity of this disease, it’s well worth the inconvenience that these pumps produce,” Dr. Bennett observed. “Once patients acclimatize to them, they’re really not that bothersome.”

Isis is exploring the possibility of pumping the oligo into the spinal fluid. From there it would diffuse into the brain. This method does not require the kind of highly invasive procedure involved in a brain insert.

Dr. Leeds pointed out that CHDI and another company are exploring a third method of delivery in conjunction: a subcutaneous shot (just under the surface of the skin). A person would receive such a shot about once a month. This technology, however, could be at least a decade off. The longest term goal would be to develop a pill.

Regardless of the methods, the patient would have to take the medication for life because of the genetic nature of HD.

Isis Pharmaceuticals’ unique flavor

Scientists began working with the concept of antisense in the 1970s, and in 2002 they discovered that oligos actually exist in nature and provoke RNA interference (RNAi). Other researchers are seeking ways to use RNAi to treat diseases, including Huntington’s. “Antisense is like a fruit,” Dr. Bennett explained. “We have apples, oranges, and pears. There’s well over a dozen different mechanisms by which you can exploit antisense to modulate gene expression.” For the Huntington’s disease project Isis is employing one known as RNase H, the name of an enzyme.

“We as a company are broadly exploiting all types of antisense,” Dr. Bennett said. “We have a little bit different flavor that we are using for this project, because in our opinion it’s working more efficiently and it’s ready for testing in man today.” The key to understanding the different “flavors,” he added, is to understand that different enzymes block or degrade the RNA in different ways. Whereas RNAi molecules are twice as large as the Isis oligo and do not enter a cell as easily, the Isis product gets get into cells without a special entryway.

If all goes as planned, after the monkey study Isis will apply for permission from the U.S. Food and Drug Administration to administer a test in a small group of humans. Following that step the company would seek a partnership with a commercial drug company to run a large-scale clinical trial. Isis will count on CHDI for establishing contact with a larger pharmaceutical company and designing an efficient large clinical trial. The Huntington’s Study Group’s “Predict HD” program, which tracks the health of people over 18 who have tested positive for HD but not yet developed symptoms, will be an important source of assistance in a large clinical trial, Dr. Leeds said.

Frank Bennett with just a few of Isis's more than 1,500 patents (photo by HDSA-San Diego) The company’s potential Isis, which has about 300 employees, will have as many as eight people working on its HD project, including chemists, biologists, specialists in pharmacokinetics (measuring the drug in tissues), toxicologists, and specialists in clinical trial development. In addition to Vitravene, the company is developing Mipomersen, an antisense drug targeted at people with extremely high cholesterol levels (500 and higher). Known as familial hypercholesterolemia, this condition is similar to Huntington’s disease because of its roots in a genetic defect. The drug could also be used for others with high cholesterol. Dr. Bennett is confident that Mipomersen will reach the marketplace. Isis has also used an antisense drug to reduce the effects of Lou Gehrig’s disease in test rodents. Isis delivered the drug, ISIS 333611, directly into the rodents’ spinal fluid via an implanted pump. The company is also starting a new project on Parkinson’s disease. Not a ‘cure,’ but a historic step for science and patients Like all other scientists, Dr. Bennett hesitates to refer to the potential HD antisense drug as a “cure.” “I don’t think we’ll cure the disease,” he said. “But what I think we may do is benefit the patients so that either we stabilize the disease and they don’t get worse, or we slow the decline…. That would be a fantastic outcome.” If the CHDI-Isis project is successful, it would be the first time that humanity brought a neurological disorder under control. According to Dr. Bennett, such a result would validate the large investment that science has made in recent years to understand how these diseases function. Isis, which began in 1989, has yet to turn a profit but has almost a half billion dollars in the bank. It expects to have a respectable operating loss of only $15 million for 2008. “We do this for the patients,” Dr. Bennett said. “These are diseases where there really isn’t much to offer those patients. We’re very motivated to provide therapies for those patients. Ultimately if we help the patients we’ll help the company. I’m paraphrasing – the CEO of Merck actually said this 40 years ago: ‘If you focus on the patients, the rest of it will fall in place.’ I truly believe that.”