Chapter Four
Camouflage Your Genes
The drugs we use today interfere with disease processes once they have started, instead of getting to the root of the problem.
In the future, though, doctors will be able to prescribe medicines earlier in a disease process, even before symptoms develop. This will be accomplished by more precisely targeting drugs, based on genetics, to smaller numbers of people with a specific set of genes, or a single mutated gene.
Doctors armed with genetic information will be more confident that the benefits of these therapies outweigh harm for a specific patient. They’ll also know when to avoid their use altogether in those patients who are genetically most likely to experience side effects.
Indeed, we have already identified some of these genes that make certain drugs safe for many, but dangerous for a few. Consider again the case of Coumadin (warfarin) discussed in Chapter One. Doctors frequently prescribe warfarin for atrial fibrillation (AF), a common condition affecting millions of Americans in their forties and fifties. AF causes one of the upper two chambers (atria) of the heart to “flutter” or fail to contract regularly, or effectively enough to push blood through the heart, into the lungs and back, and then out to the rest of the body. People with AF end up feeling breathless and fatigued. In addition, blood can pool in the ineffective atrium and clot. These clots may then dislodge and travel to the brain where they cause strokes, or travel to the lungs where they cause fatal pulmonary emboli, a common cause of sudden chest pain and death. Warfarin can prevent these blood clots from forming.
Two genes determine how well a patient fares on warfarin. CYP2C9 controls a liver enzyme responsible for breaking down warfarin, and VKORC1 determines how sensitive you are to it. It turns out that warfarin complications arise from just eight variations in the CYP2C9 gene and one in the VKORC1 gene. In most cases a single nucleotide change determines whether warfarin works at all, works properly, or works too well.
In order to use the drug, doctors must administer a dose, monitor how quickly blood clots, and then painstakingly alter the dose until the blood clots quickly enough to prevent uncontrolled bleeding, but not so fast that clots form in the bloodstream. The body takes several days to respond to such changes.
Meanwhile, other drugs or even diet can affect warfarin level and activity. It’s no wonder side effects of warfarin are responsible for one in ten hospital admissions in the U.S. costing the healthcare system over one billion dollars per year.
But now, prescribing warfarin may be guided by whether you have one of the mutations for these two genes, and the right dose more easily selected.
Prescribing small molecule drugs or biologics to more discreet populations is one obvious benefit of the advances made in unraveling the human genome. Designing new drugs based on trying to camouflage errors in the genome, genetic mutations, is another option that is now rapidly coming into play.
Nowhere will the ability to develop specifically targeted new drugs have more impact than for patients suffering from rare diseases. These estimated 14,000 distinct rare diseases differ greatly, but when taken together, a rare disease affects one in ten Americans, so it’s likely that you know someone with a rare disease, whether you’re aware of it or not. Approximately eighty percent of these rare diseases arise from defects in a single gene, and half of them affect children.
This single gene defect usually prevents the body from making a critical protein. When that protein serves as an enzyme, catalyzing vital biochemical reactions, replacing the enzyme becomes a valid treatment approach.
Several diseases can be treated this way. One example is Pompe’s disease, which causes glycogen to accumulate in skeletal muscle and weakens the heart muscle. This ailment responds to the replacement of the enzyme, acid alpha-glucosidase.
Another ailment, Gaucher’s disease, caused by the accumulation of certain fatty molecules, is treated with infusions of the glucocerebrosidase enzyme.
Enzyme replacement strategies work, but they aren’t convenient. They must be administered regularly for the rest of your life. And many enzyme replacement therapies require intravenous infusions. In addition, in order to remain active, enzyme replacement therapies must be stored in carefully controlled environments.
Not only that. Enzyme replacement strategies can’t address all single gene rare diseases because it may not be possible to get the drug to where it is needed inside the body.
For most diseases a better strategy would be to correct the protein defects when and where they are made.
But how do you do that?
The answer starts with RNA. The evolution of the RNA molecule is the reason we exist today. Life on earth, from the simplest bacterium to human beings, would have been impossible if RNA molecules hadn’t been formed in the hot reactive stew of the primordial soup. They not only formed, but began to react with each other until they started replicating themselves. From RNA came DNA and protein. And with that, a sterile planet possessed the building blocks of life.
Throughout evolution, RNA has maintained its central role. Not merely as a go between, but an active, if mostly unseen, participant in any organism’s life processes. That central role makes RNA the perfect location for some very targeted medicines.
Science first took notice of this complex but fragile molecule at the turn of the last century. By mid-20th century, the idea that RNA served as a messenger for protein production began to take hold. By the start of this century, science revealed critical roles for the molecule in biology, involving gene regulation, protein manufacture, and aging, among others.
The pace of research regarding this key molecule has accelerated since Andrew Fire and Craig Mellow received the Nobel Prize for Medicine in 2006, for work reported in 1998, that genes could be silenced by interfering with their RNA.
At the turn of this century, according to Muhammad Sohail, editor of the Journal of RNAi and Gene Silencing, there were only 70 to 80 papers in this esoteric field, but midway through the last decade, the number had leapt to 70 to 80 every hour! Over the same period the number of biotech companies looking to exploit this evolving science has also rocketed.
Because RNA is the link between the cell’s instructions housed in the nucleus and its activity beyond in the cytoplasm, interfering with or altering RNA’s function can have sweeping impacts on how the cell interprets the instructions from its own DNA.
Knowing how to interfere with RNA opens the door for us to prevent disease before it can begin.
There are a number of different strategies for doing this. They all rely on the RNA molecule’s similarity to DNA.
DNA exists as two long separate but intertwined strands held together by weak bonds of attraction between complementary bases, adenine (A), cytosine (C), guanine (G), and thymine (T). The genetic code arises because A always pairs with T and C always pairs with G.
RNA, on the other hand, is a single-strand molecule comprised of the bases adenine (A), cytosine (C), guanine (G), all of which are part of DNA, and uracil (U), a base that is very similar to thymine. While RNA is a single strand, it loops around and folds back on itself in such a way that A always pairs with U and C always pairs with G. As noted in the last chapter, the fact that both molecules are comprised of complementary bases means that the mobile RNA can ferry out (from the cell’s nucleus) the genetic information contained in the stationary DNA.
The ability of RNA and DNA to bind to each other can be exploited to interrupt cellular processes by employing very small snippets of DNA called oligomers or oligonucleotides. Whereas a single human gene is, on average, comprised of at least three thousand nucleotide units, an oligomer is usually comprised of ten to thirty units.
When an oligomer binds to RNA, it can interrupt cellular activity. That proves useful when a cell’s activity has gone awry.
In 1978, Paul Zamecnik and Mary Stephenson, both of Harvard University Medical School, created the first active oligomer aimed at a virus that causes cancer in chickens.
That virus was first discovered by Peyton Rous of the Rockefeller University in 1911. Rous took a tumor from a chicken, ground it up with salt water and filtered it through such a fine filter that no cells, either chicken or bacteria, remained. Rous then injected the “cell-free” extract into chickens. The injected chickens developed a type of cancer, a sarcoma to be exact. He dubbed whatever agent was causing chicken cells to transform into cancer cells the Rous Sarcoma Virus. It was the very first virus discovered that causes cancer. Rous received the Nobel Prize in Physiology or Medicine over fifty years later, in 1966, as a result of this discovery.
In the time between the discovery of the Rous Sarcoma Virus and Zamecnik and Stephenson’s experiments, it had been established that viruses are comprised of some structural proteins and genetic material, either DNA or RNA, and that they rely on the cellular machinery of the host cell, the ribosome, to produce proteins. The Rous Sarcoma Virus in particular is an RNA virus.
Zamecnik and Stephenson prevented the Rous Sarcoma Virus from transforming chicken cells into cancer cells. They used a 13-base oligonucleotide that bound to the RNA of the virus. This was the first time a small DNA molecule, complementary to a section of RNA, was used to interrupt cellular processes. The oligonucleotide bound to the viral RNA preventing it from engaging the chicken’s ribosome. This stopped the chicken cells from producing the proteins needed to cause the cancer to form and grow.
The experiment by these Harvard scientists marked the birth of “antisense therapy” and made it possible to make targeted medicines (Figure 2.1, #11).
As mentioned in the previous chapter, copying instructions from DNA isn’t an entirely straightforward activity, at least for creatures more complex than bacteria. When the cell needs instructions from DNA, an enzyme in the nucleus known as RNA polymerase (Figure 3.3) begins to copy the instructions by peeling open the strands of DNA and manufacturing a strand of RNA, base by base, that is the perfect complement to the unzipped DNA strand; every A on the DNA is incorporated as a U in RNA, every C in the DNA is represented by G in the RNA, every T in the DNA becomes an A in the RNA and every G in the DNA shows up as a C in the growing RNA strand.
The problem is that, like in any good book, first drafts need a bit of editing. Genes don’t reside on the chromosome in one contiguous piece. Interspersed throughout are sections of DNA that don’t code for protein. In most cases we don’t know yet what these sections do.
In order to make a protein, the cell must edit out all of these nonessential sections, called introns, from the growing strand of RNA and splice together only the protein coding portions, called exons. The RNA cannot move out of the nucleus as a mature message for the protein coding machinery, the ribosome, until all of the introns are removed.
While it still has introns, the RNA is a pre-messenger molecule, and is confined to within the nucleus.
For a surprising number of diseases, especially rare diseases, a single defect in just one of those exons is enough to cause the protein manufactured to fail to work properly. Sometimes, the defect will cause the ribosome to stop dead in its tracks and fail to make the protein altogether.
According to the World Health Organization, ten babies in every one thousand have a single gene disease, with over four thousand diseases caused by a single defective gene. A Canadian paper (Scriver, 1995) reported that so called monogenic disease may be responsible for up to 40% of children being seen in hospitals.
Some cases of cystic fibrosis and Duchenne muscular dystrophy are caused by these “nonsense” mutations that stop the production of protein. The mutation can be a single nucleotide change in just one of the DNA’s exons.
We also know that in seventy percent of neurological disorders, the process of splicing the exons together has failed or is altered.
Other times, the instructions dictate that the cellular machinery incorporates the wrong amino acid into the growing protein and the protein folds improperly. It becomes useless or imperfect, affecting other cellular processes.
For example, take sickle cell anemia. A change of a single base of DNA causes the wrong amino acid to be inserted into the hemoglobin protein. In this case, valine is inserted instead of glutamic acid. Valine and glutamic acid couldn’t be more different. Glutamic acid, the correct amino acid, is water loving, while valine, the wrong one, abhors water.
When valine is inserted into hemoglobin protein, the surrounding water in our bodies repels it and distorts the shape of the protein. As a result, the red blood cell becomes elongated, sickle-shaped and stiff, rather than the normal flexible, round, and smooth doughnut shape. That sickle-shaped cell gets stuck in small blood vessels. In addition, sickle cells fail to carry oxygen efficiently, causing painful crises for those who suffer from the disease.
Since the early 1970s when Theodore Friedman and Richard Roblin first suggested that defective DNA could be replaced with “good” DNA, scientists have been working on “gene therapies” to do just that.
Many scientists have focused on replacing genes wholesale by inserting a new, correct copy of the gene into cells using viruses as the carrier. It’s a thought-provoking approach. However, researchers have run up against several obstacles. Getting the gene into the cells that need it, avoiding the body’s immune defenses, and finding a way to make the gene function properly have all been huge challenges.
Other work has focused on inserting stem cells into host tissue where they can mature into healthy versions of the adult cells and replace the diseased cells.
At the same time, building on Zamecnik’s work with Rous sarcoma virus, other scientists have started attacking the problem of faulty DNA, not by fixing the DNA, but by blocking the message coming from that DNA from being transmitted. In other words, camouflaging or patching the message.
As of this writing, we don’t know how to go into a cell and correct a small defect in a strand of messenger RNA. That doesn’t mean we can’t camouflage the message using the same “antisense” therapy that Zamecnik employed. In the same way you use makeup to be more attractive, the message from the gene in the nucleus can be camouflaged to be more “attractive” to the ribosome in the outer part of the cell.
The first way to stymie damaging RNA, either from disease causing genes or from acquired viruses, is by destroying their message. Zamecnik showed that when an oligomer was attached to Rous sarcoma virus RNA, the virus failed to replicate itself and couldn’t cause cancer.
Here’s why that effort was successful. When the DNA oligomer binds to the viral RNA, the ribosome can’t manufacture proteins. The enzymes, which are constantly seeking to tidy up stray bits of bound nucleic acids, destroy both the RNA and the oligomer binding to it. The protein manufacturing system is free and able to respond to other messenger RNA strands. The message is blocked.
Scientists use this technique either to stop a defective protein from being made or to damp down the excessive manufacture of a protein that is harmful to the body.
While destroying bad messages will suppress the production of disease causing proteins, the same process won’t help if you want to start the supply of a missing, functional protein. To generate the protein, the ribosome needs to get the instructions.
The second way to prevent RNA causing disease is to change, or camouflage, the message it conveys. By aiming small bits of antisense DNA at pre-messenger RNA, we can create slight changes to the mature messenger RNA that leaves the nucleus, thus altering what happens in a cell. The RNA is not destroyed, and neither is the oligomer, because the enzyme clean up team does not recognize it and fails to tidy it up. The message gets through to the ribosome but it has been altered, beneficially.
Scattered throughout the genes that encode for proteins are sections of information unnecessary for producing those proteins, the introns. These oligomers take advantage of that fact. When mature messenger RNA is transcribed from the DNA template, it must first knit together the protein coding exons and cut out the non–coding introns. This process is called splicing. After splicing, the messenger RNA can move from the nucleus to the protein producing ribosomes in the outer part of the cell.
A collection of proteins and small nuclear RNAs accomplish this task by identifying where each exon and intron starts and stops on the strand of pre-messenger RNA. They must cut the pre-messenger RNA at the precise boundary between each exon and intron. Finally, they splice together the exons in the correct order. Though this process may sound complicated, the cells in our bodies splice messenger RNA millions and millions of times a day.
While they have the ability to splice out introns and the information they contain, the cells can’t excise defects found within exons. Any problems in the coding sections for proteins remain once the mature messenger RNA has been spliced together. If the problem within the exon leads to a minor change from one amino acid to another that shares similar chemical properties, the result could be imperceptible. For example, a water-loving amino acid could be swapped for another water-loving amino acid by the ribosome.
If the amino acids exchanged are more dissimilar, as in the defect associated with sickle cell anemia, the protein may not function correctly and could cause disease. If the defect in a particular exon causes the ribosome to stop making protein altogether, it will almost certainly cause disease.
However, what if a protein doesn’t actually need all of the amino acids in the complete protein for it to be active and viable? What if entire exons could be hidden from the splicing process? In the earlier analogy about a car, it might still work and be drivable but have a coat of paint missing or a different radio.
A shorter strand of messenger RNA would result, without the defective exon, and an active, or even partially active protein could still result. In that case, finding a way to skip over an exon with a defect may allow a new, functioning protein, albeit slightly shorter than the natural protein, to be produced. This would be especially true of a defect that orders the ribosome to stop during the processing phase.
It turns out that the cells in our bodies “skip” exons all the time. That truth flies in the face of genetic dogma established in the 1930s and 1940s, when it was thought that one gene produces one protein, often an enzyme. However, for possibly 95% of multi-exon genes, the cell can splice messenger RNA together in several remarkably different ways.
Take, for example, the hormone calcitonin, which is produced by the thyroid gland and is critical for the regulation of calcium in the bloodstream. The calcitonin gene contains 6 exons. However, in order to produce calcitonin, thyroid cells splice down the pre-messenger RNA so that the mature message includes only exons 1, 2, 3 and 4 (Figure 4.1)
That doesn’t mean exons 5 and 6 serve no purpose. Different cells in the nervous system take the same pre-messenger RNA produced from the calcitonin gene and skip exon 4. By splicing exons 1, 2, 3, 5 and 6 together to make a different mRNA, the ribosomes for the nervous system generate a different protein product, alpha-calcitonin gene-related peptide, or a-CGRP, that relaxes blood vessels.
Another example of normal alternative splicing occurs in the AMPA receptor that was described first by Danish medicinal chemist and neurobiologist, Tage Honore, in 1982. AMPA stands for alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid. It is a very important receptor in the brain, composed of four subunits which each have two forms – a “flip” form which makes the AMPA receptors have high activity, and a “flop” form which makes low activity receptors. The flip and flop forms are mutually exclusive and are formed by an alternatively spliced section of the pre-mRNA - either splicing out exon 3 but leaving exon 4 in the mature mRNA or splicing in exon 3 but leaving out exon 4. The high activity AMPA receptor leads to excessive excitability of the central nervous system, causing diseases like epilepsy or amyotrophic lateral sclerosis or ALS (Lou Gehrig’s disease).
Figure 4.1. An example of alternative splicing. The calcitonin gene is composed of six exons. In the nucleus of thyroid gland cells, exons 1, 2, 3, and 4 are spliced together, the mRNA leaves the nucleus and the ribosome generates calcitonin from these instructions. The same pre-mRNA strand in the nucleus of nervous system cells has a different fate. Exons 1, 2, 3, 5, and 6 are spliced together to form a different mRNA strand that leaves the nucleus, is then read by the ribosome and leads to the generation of alpha-calcitonin gene-related peptide.
Several other nasty neuromuscular diseases are linked to mRNA splicing defects, so the opportunity to effectively, safely, and consistently alter splicing beneficially has wide ranging implications.
Sometimes, skipping an exon doesn’t necessarily change the job a protein does. Instead, it affects how well the job gets done.
Alternative splicing is not just confined to humans. All animals and plants utilize alternative splicing to make multiple proteins from any single gene. Much of the scientific work on alternative splicing has been done in Arabidopsis, a small, annual, spring flowering plant from Europe, Asia and northwest Africa. Because Arabidopsis has a relatively short life cycle of six weeks, and a small genome of only 157 million base pairs, botanists and geneticists routinely use it to study alternative splicing.
The fruit fly has also been an important research subject. An extreme example of alternative splicing was described in 2004 where it was found that a single gene of the fruit fly, Dscam, gives rise to 38,016 different mRNA variants and proteins.
Because alternative splicing is well documented in nature, it makes sense that modern medicine would attempt to trigger that mechanism to produce effective proteins.
By using oligomers, we can alter the way a pre-messenger RNA splices together its exons. RNA splicing takes place when a collection of RNA/protein complexes recognizes a specific sequence of bases, the four letters A, C, G and U, at the interface between introns and exons as well as sequences within the intron. These complexes, called spliceosomes, cause the RNA to loop around, putting the exons in close proximity to each other. Then, they cut the intron out and stitch, or splice, the adjoining exons together.
If the pre-messenger RNA doesn’t contain the specific bases signaling the junction between an intron and an exon, the spliceosome can’t recognize it and can’t splice together the correct exons. That’s where therapeutic oligomers come in. Suppose you have a gene with six exons and five introns, of which exon 4 contains a nonsense mutation that you want to skip in order to make a functioning protein. By creating an oligomer that is complementary to the splice site at the beginning of exon 4, you can effectively camouflage or mask that splice site from being recognized by the busy spliceosome.
When the spliceosome begins processing the pre-messenger RNA, the oligomer will hide exon 4.
Instead of splicing exon 3 and exon 4 together, the spliceosome will create a messenger RNA comprised of exon 3 spliced to exon 5, skipping exon 4 altogether. The protein will then be shorter, missing the amino acids that would have been coded for by a non-mutated exon 4, but potentially retaining important activity.
In fact, it is possible to produce an effective protein with missing sections. Doing so offers the opportunity to address some of the most vexing genetic conditions that afflict humans today.
But how did we get to the point where we can literally defy our DNA?
In the century and a half since an Augustinian friar nudged open the door to the age of genetics by publishing his efforts to breed sweet peas, medicine has changed dramatically. At the same time that Gregor Johann Mendel (1822-1884) was untangling the basic tenets of genetic inheritance, Louis Pasteur (1822-1895) was first proposing the idea that infections, the principal killer at the time, were caused not by an imbalance of humors, but the spread of germs. That theory spawned medical advances that include sanitation, aseptic surgical techniques, and antibiotics, as well as the pasteurization of milk that pays tribute to the great Frenchman. It is not an overstatement to say that these advances have resulted in decades being added to the life expectancies of people living in developed countries.
Mendel’s work on genes, however, is only now beginning to provoke such a revolution. His efforts moldered for roughly thirty years before they were rediscovered and applied to understanding human inheritance and genetic conditions. It took another forty years before scientists were certain that DNA was the source of genes and inheritance in humans. Not until Watson and Crick announced the structure of DNA in 1953 did the pace of genetic discoveries begin to accelerate. Researchers went from describing the central dogma that DNA stores genetic information and RNA provides the template from which proteins are made, to deciphering the genetic code and identifying the specific genetic defects associated with disease.
Though the field of genomics started 150 years ago, it has not yet been fully integrated into drug development. Until now, that has proven prohibitively expensive and time consuming.
But that’s changing.
This change is important because the field of drug development is rife with stories of drugs that show remarkable promise in early studies, until serious, but rare side effects show up when the drug is tested in larger groups of patients. Historically in these situations, pharmaceutical companies often halt development or pull the drug off the market.
But everyone involved with the creation of the drug wonders what made it work so well for some yet prove dangerous for others.
Let’s take a look at the story of Vioxx.
Vioxx is a non-steroidal anti-inflammatory drug (NSAID) that was often prescribed for arthritis. It’s like aspirin and ibuprofen, as well as more than thirty other effective drugs that share the common and serious side effect of stomach ulcers.
But unlike the others, Vioxx doesn’t cause ulcers. Here’s why.
The body uses inflammation as the first line of defense in fighting infection. A critical step in the inflammation process is the production of the chemicals prostaglandin and thromboxane, employing two different pathways, cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2). Most cells in our bodies employ the COX-1 pathway that is essential for the cells to be healthy. The COX-2 pathway turns on only in specific cells in areas of inflammation, especially when joints are inflamed.
NSAIDs work by blocking both COX pathways. Stifling the COX-2 pathway effectively reduces joint inflammation. But the stomach relies on prostaglandin to protect it from stomach acid and inhibiting the COX-1 pathway reduces the level of protective prostaglandin in the stomach lining, leading to irritation, ulcers, and in severe cases bleeding or perforation.
The scientists who created Vioxx hoped that blocking only the COX-2 pathway might reduce the inflammatory prostaglandins and thromboxane while protecting the stomach by leaving the COX-1 pathway unaffected.
In 1998, Merck submitted a new drug application documenting all of the laboratory, animal and human testing data pertaining to the development of Vioxx. In 1999, the FDA approved Vioxx for sale in the U.S., with the caveat common to most drugs: that the company formally study it over a longer period of time in more patients in addition to the standard requirement to monitor sales, collect data on side effects, and report back.
Post approval studies are designed to test drugs in “real life” settings thereby helping to define the true incidence of rare side effects. Merck conducted several such studies. In 2000, the New England Journal of Medicine published the results of the Vioxx gastrointestinal outcome research study. It suggested a small, but significant, increase in the risk of heart attack over twelve months. While only one out of every thousand taking the traditional NSAID, naproxen, had a heart attack, with Vioxx, four out of every thousand suffered that fate.
Despite warnings about this increased risk, by 2003, Vioxx reached blockbuster status, with annual sales of $2.5 billion.
The following September, Merck concluded that the risk of a heart attack was simply too high and voluntarily removed Vioxx from the market. The results of other studies haven’t conclusively answered whether the risks for heart disease outweigh the benefits of reduced stomach ulcers. In 2005, regulatory panels in the U.S. and Canada urged Merck to bring Vioxx back with a specific warning about heart attacks. Merck declined.
When scientists developed the COX-2 inhibitors they didn’t appreciate that by blocking the COX-2 pathway alone, they might be altering the balance between prostaglandins and thromboxane throughout the body, including in the heart and blood vessels supplying the heart.
Yet, the question remains: Why did the Vioxx work well for so many patients but cause grievous harm, in this case a heart attack, to a select group?
So far, nobody knows. I believe it is likely that a gene controls this outcome. Once identified, the availability of personal genome sequencing will permit physicians to predict if any of the COX-2 inhibitors are likely to cause a heart attack and prescribe just to those not at risk.
When such a gene is discovered, it will probably be too late for Vioxx.
Many blockbuster drugs cause rare or common side effects as a result of personal genetic differences. Four drugs, the antidepressant fluoxetine (Prozac), the anti-acid reflux drug Propulsid, the diabetes drug Avandia and macrolide antibiotics similar to erythromycin, can alter the electrical changes in your heart, prolong the QT interval and in rare circumstances cause heart attacks.
Scanning the genome for genetic predisposition to side effects can and will become standard practice during drug development and in routine clinical care as medicine advances and becomes more personalized.
QT Interval Prolongation
If you have a mutation in a gene that regulates the electrical activity of your heart, taking Propulsid or erythromycin can provoke a heart attack. The genes that put you at risk, KCNQ1/KCNE1 (LQT1) and NaV1.5 (LQT3), follow the rules of dominant inheritance. You only need to inherit one gene from one of your parents in order to be at risk of a heart attack from taking erythromycin.
The electrical record of a heart contraction, the electrocardiogram, has several distinct peaks and troughs on it, called the P wave (the electrical wave spreading across the upper chambers or atria), the QRS complex (the electrical wave passing through the muscle of the ventricles causing them to contract and pump the blood out and into the lungs and around the body) and the T wave (the heart muscle re-polarizing in preparation for the next beat). The shapes, amplitudes and durations of these various electrical waves, and the interval between them, are well defined. Changes to any one of these parameters can indicate disease.
Propulsid, after it became generally available, was recognized as a drug that could, for some people, lengthen the interval between the Q and T waves, sometimes causing fatal changes in electrical activity in the heart. As a result of that increased knowledge, all new drugs now have to undergo testing to see if they cause QT prolongation. Propulsid was withdrawn from the U.S. market in 2000 because there are alternative drugs that can be used to treat acid reflux. Still, screening for these genetic conditions becomes important if you have an infection that could respond to erythromycin. Then, your doctor could use the tools of genomics to predict if you are at risk of side effects before deciding whether or not to prescribe it.
Some of those abandoned drugs could be resurrected if a genetic cause for their side effects could be identified. That would provide a test to ensure the drug is safe for an individual patient. This is expensive, time consuming, and not readily available until now. In the future, more companies will attempt this if the drug in question promises to meet a hitherto unmet medical need.
With the cost of genomic sequencing rapidly declining, genetic information will become a critical component of clinical trials for all potential new drugs, not just those with an already identified rare adverse effects. As some patients respond positively to a particular agent and others develop side effects, the researchers conducting the trial will search for genetic differences as a possible explanation. If genetics is indeed the cause, when a company submits the data for a new drug for approval, they will document who is genetically most likely to suffer. When the drug comes to market, physicians will be able to tailor their prescriptions to the genetic makeup of the individual patient.
At that time, the era of the blockbuster drugs will be over. Precisely identifying genetic profiles means that pharmaceutical companies will develop new drugs for smaller groups of patients. They will specifically target the genetic source of disease and develop drugs that can stop a disease literally at birth. New drugs will treat fewer patients, but each patient will be treated for longer and from a younger age, with greater safety, to prevent the disease in the first place.
We are truly on the path to a “predict and prevent paradigm” of personalized medicine.
Some day in the future, everyone who is born will be given both a birth certificate and a genetic map. At that time, we will be able to address some of the most vexing inherited conditions that afflict humans today.
In so doing, we will indeed be able to defy our DNA
Summary
Over the 35 years since Zamecnik experimented with the first oligonucleotide to block viral RNA, we have come a long way. Alternative splicing is now understood to be the body’s way of translating 25,000 genes into 150,000 proteins.
A single altered gene, exon or even nucleotide can have fundamental and lethal effects. Modern medicine is now developing the necessary tools to effectively start turning the tide on these faulty genes. Therapeutic oligomers will allow us to effectively treat diseases, even before their message leaves the nucleus on its way to the cellular factory.