The 2 billion dollar protein sequencing error

11 Jul 2010 // protein

Have you ever made a sequencing error? Remember the moment you finally stare at the control experiment, and it slowly dawns on you that you had really fucked up. You stomach drops as you realized the consequences: maybe you kick yourself for your stupidity, maybe you just realized that you had poured 12,000 dollars down the drain, maybe you had just seen a chapter in your thesis dissolve into thin air. But anything you might imagine will pale in comparison to the sequencing error made by a company in the wild-west days of biotech.

You've probably never heard of the company that made the error (Genetics Institute). The company that did not was Amgen. And the difference is a patent now worth $2 billion a year. The protein involved is known as erythopoietin, but you probably know it as the drug that Lance Armstrong did not take, otherwise known as EPO.

It's a sordid but rather entertaining story (would make a decent screen-play), and I stumbled on to it whilst Merrill Goozner's history of the modern pharmaceutical industry "The $800 Million Pill: The Truth behind the Cost of New Drugs". Not only did the sequencing error set back Genetics Institute in the race to patent the synthetic manufacture of EPO, but Genetics Institute had actually stolen the sequence from Amgen in the first place.

But first, some background.

The golden age of biotech in the 1980's centered around a cluster of technologies now known as recombinant DNA engineering. In recombinant DNA engineering, if you could extract the complete DNA sequence that coded for a protein in the human genome, you could recombine that piece of DNA into a virus, inject that virus into a colony of bacteria, and force feed the bacteria into making industrial quantities of your human protein. This was much easier than the previous method, which is to kill a lot of animals and extract minute quantities of the protein, and make medicine out of it.

This promised a dramatically new line of therapy for diseases caused by the lack of a specific protein; the replacement of which restored normal function in a sick person. In hindsight, it turned out that there were only a handful of human diseases – the "low-hanging fruit" of biotech – that could fit this description. But almost every one of these diseases would lead to a blockbuster drug that would make the fortune of several biochemistry professors of the US university system.

Erythropoiesis – or red blood cell formation was one such disease. Red blood cell formation was known to be triggered by the presence of one, and only one, protein; erythopoietin or Epo. When Winston Salser left UCLA to create AMGEN, he had no clear idea of what he wanted to work on. He chased several drug targets of diseases, one of which, included erythropoiesis. However, for him to apply his DNA recombinant techniques to Epo, he would need the DNA sequence. And that, he did not have.

Cue to Eugene Goldwasser, who over several decades, had worked out methods to identify EPO, and purify it; first from animals, and then from humans. However, he did not know the protein sequence, let alone the DNA sequence that codes for the protein. Indeed Goldwasser didn't even have that much Epo. It wasn't until 1973 that Goldwasser found a way to produce workable quantities of Epo. Goldwasser was contacted by Takaji Miyake of Kumamoto university, who had access to some patients who suffered from a condition called aplastic anemia. The bone marrow of these patients did not work properly and led to an overproduction of Epo in the patient's urine. Sending this urine to the US, Goldwasser was able to purify 8 mg of pure human Epo from 2,250 liters of piss over a period of 18 months. This became the world's only supply of Epo.

After a lot of delicate negotiations, Goldwasser did a deal with Amgen. And Amgen undertook the process of figuring out the DNA sequence for EPO in the human genome, using Goldwasser's store of Epo. You might be aware from first year biochemistry that there is a unique DNA code for the amino acids that codes for a protein. But a working gene, or fully functioning DNA sequence, includes so much more: start codes, end codes, promoters, repressors, splicing points, and other such regulatory pieces of DNA. Consequently, the process involved, first, working out the protein sequence of Epo, then working out the DNA sequence that codes the amino acids, and finally using fragments of these sequences to search for the actual piece of DNA in an actual human genome.

But first, Amgen needed the protein sequence of Epo. And they were in luck. In this golden age of biotech, many new machines would spring into existence like Athena from the head of Zeus. Leroy Hood of Caltech had just built a machine that could sequence the amino acids of a protein, any protein, using only a small quantity of protein. So Amgen sent a small sample of Epo to Leroy Hood to figure out the protein sequence.

And here is where it gets interesting. Rodney Hewick, one of the co-inventors of the protein sequencing machine, was one of the people who carried out the sequence analysis. After sequencing Epo, Hewick abruptly quit on Sep 1st 1981, only to immediately join a Boston biotech, Genetics Institute as a senior protein chemist. He arrived at the new company bearing gifts, and the gift was the sequence of Epo.

Suddenly the race was on for the identification of the human gene of Epo, and the patenting of the process to synthetically manufacture EPO using DNA recombinant engineering: Amgen on the West coast, Genetics Institute on the East coast.

The problem was that Rodney Hewick made exactly 3 errors out of 166 amino acids in the protein sequence of Epo. And he didn't even know it. And in Boston, he had no more access to Goldwasser's precious store of Epo to double-check his sequencing. After 3 year of failure, Genetics Insitute finally realized that their protein sequence was wrong. To mitigate their error, they had to hammer out a deal with Miyake in Japan to get their hands on the precious urine of the patients with aplastic anemia. They purified their own Epo, sequenced it again, and finally found the full gene for Epo. They submitted the article to Nature on Dec 7, 1984.

But by then it was too late. Fu-Kuen Lin, who had joined Amgen as their 7th scientist in 1981, had single-handedly identified the human of Epo in the human genome using Goldwasser's protein. More important than getting a Nature paper, he had filed a patent for Amgen in Dec 13. 1983, a good year before Genetics Institute's Nature article. In the world of big pharma, it is the patent that matters. Amgen got FDA approval in on June 1 in 1989. EPO was Amgen's blockbuster drug, which attracted 460 million dollars from the government in the first year. It is now worth 2 billion dollars of income, and almost half of Amgen's income in 2002.

Amgen became a biotech behemoth, whereas Genetics Institute eventually got bought out by Wyeth. And all because of of 3 errors in the sequencing of the protein.