6.8.16 | YouTube
The view from 30,000 feet
- What is cancer?
- Cancer is unique among diseases
- Over 3 million PubMed papers under the search term “cancer” (circa 2016)
- Cancer Genome Atlas (TCGA)
- Emerging Theories of Cancer
- Cancer 2.0 — cancer as an orderly epigenetic disease
- The importance of hexokinase 2 (HK2) in the cancer’s metabolic phenotype
The somatic mutation theory has dominated cancer biology for almost 50 years
“Cancer, we now know, is a disease caused by the uncontrolled growth of a single cell. This growth is unleashed by mutations — changes in DNA that specifically affect genes that incite unlimited cell growth (Mukherjee, The Emperor of All Maladies, 2010).”
“The Scientists say that bad luck plays a stronger role in some cancers than in others. In two-thirds of the cancers — 22 cancer types — random mutations in genes that drive cancer could explain why the disease occurred (The Guardian, January, 2015 CKTK).”
The somatic mutation theory of cancer
- Simple initiating mutator mutation
- Sequential, multi-step mutagenesis and selection
- Wind up with a tumor
The Cancer Genome Atlas
The Cancer Genome Atlas — Breast cancer example:
- Sequenced the tumors of 100 women with breast cancer
- These are the genes they determined to be the driving genes
- If they can’t determine through functional data, it’s the frequency of the mutation
- These are point mutations, copy mutations, but the important part — what caught everyone off-guard — was the huge degree of intertumoral heterogeneity from one patient’s tumor to the next
- There are very few commonly mutated genes
- The other thing that caught people off-guard was that there were many samples with single driving mutations, two driving mutations, or ZERO driving mutations
- So it’s impossible to reconcile a genetic origin with this data.
- How can there be zero driver mutations in cancer?
There is a strikingly high degree of intertumoral heterogeneity (i.e., the degree of mutational difference that exists from person to person) and intratumoral heterogeneity (i.e., the degree of mutational difference that exists within the same tumor, from cell to cell)
Cancer Genome Landscapes
Paper by Vogelstein’s group (Vogelstein et al., 2013 CKTK)
- Bert Vogelstein wrote a review asking this question: Where are the missing mutations?
- He goes on to describe what he calls dark matter
- There’s some presumptive force that we’ve yet to identify that’s driving the disease
Problems with the somatic mutation theory
- Missing mutations — Impossible to reconcile neoplasms with few to no driver mutations
- Ad hoc addition of mutator mutation (like Tom said: bank teller analogy) — when you measure the mutation rate within human cells, it’s very low
- >> It’s impossible to reconcile the rates of cancer with the known rates of mutation
- >> They modified and said that the first mutation must be in the gene that controls DNA repair
- >> This allows for the probability fo other mutations to occur
- >> Impossible to explain tremendous “gain of function” by rendering biological system dysfunctional
- >> Systematically wiping out biological systems
- >> Dramatically illustrated in TCGA ancillary study looking for genes that correlate to metastasis
- >> The most important feature of cancer
- >> They found zero
- >> They couldn’t correlate a single mutation to metastasis
- >> And that’s what the Hanahan and Weinberg model presupposes: every hallmark of cancer is driven by oncogenes
- >> But they can’t find them
New theories have emerged explaining cancer
The metabolic theory
- Explains the genetic heterogeneity observed in most solid tumors
- Explains the consistent reversion to fermentation (the Warburg effect)
- Explains how neoplasms can exist with two or fewer drivers
- Casts cancer as an epigenetic disease
- Explains the tremendous gain of function observed in cancer
- Agrees with the series of nuclear transfer experiments
The Tissue Organization Field Theory (TOFT)
- Explains confusing sequencing data
- Agrees with series of experimental data testing stroma/epithelial interaction after exposure to a carcinogen
- Explains “gain of function”
- Casts cancer as an epigenetic disease
- The default state of epithelial cells is cell division
- The epithelium is kept in check by the tissue architecture field
- Exerts negative controls to keep the epithelium from dividing
- Once that relationship breaks down, the epithelium begins neoplastic growth
- Explains the confounding data from the Atlas project
- Agrees with a series of convincing experimental data testing stroma/epithelium interaction after exposure to a carcinogen
- When you apply a carcinogen to the stroma and disrupt this architecture and then recombine epithelial cells that haven’t been exposed to a carcinogen, you get cancerous growth
- When you flip it: hit epithelial cells with a carcinogen, put them back into intact architecture, and neoplasm is suppressed
- Casts cancer as an epigenetic disease
Paradigm shift — “cancer 2.0” — epigenetics
- Combined in the notion that cancer is driven by a predetermined subroutine
- Shifting the perception that cancer is a disease of order rather than a disease of disorder
- Process driven by epigenetic changes
Raises a big question: why would all life have a “cancer subroutine” preloaded in its DNA?
Why would all life have a cancer “subroutine” preloaded in its DNA?
The Atavistic Model of cancer
It’s deterministic, systematic, unfolding some preprogrammed response: what gives?
- Recent answer: the atavistic model by Paul Davies and Charlie Lineweaver
- An evolutionary throwback: we all have it within us, but it’s suppressed
How life populated the planet
- Formed 4.6 billion years ago
- Life began about 4 billion years ago
- Begins as unicellular life: simple biological imperative is to replicate (replicative immortality)
- About 1 billion years ago, cells begin living in clumps: multicellular life
- They signed a contract with each other (Nick Lane line about
- Repressed multicellular replicative immortality for the good of the collective
- Speciation took off
- Unicellular ==> Colonial ==> Multicellular
- Species don’t reinvent themselves anew: they build on old programs
Each layer of capabilities is built on, and depends upon, the earlier layers
Davies calls the “bells and whistles of evolution” the newest capabilities to evolve — big brains, etc — but embedded in all of this, the earliest capabilities are still there, which is replicative immortality
Development of a whale
Begins with fertilization of an egg:
- Cells trickle down Waddington’s epigenetic landscape towards terminal differentiation
- An idea in developmental biology that ontogeny recapitulates phylogeny: embryogenesis reflects our evolutionary sweep across the planet
- The earliest genes we express are the first genes to have evolved
- The lates genes, the terminal differentiation genes, are the newest genes to have evolved
- The whale undergoes the developmental program of legs
- Because a whale evolved in an ocean, it suppresses that program
- Occasionally that suppression system breaks down and you get an atavism: whales with rudimentary legs
- We see atavisms in nature all the time
- Snakes with legs
- Humans with little tails or webbed feet
Development of cancer
We can look at cancer in this same context: an atavism
- Life begins with a fertilized egg
- Totipotent cells which trickle down towards terminal differentiation
- Some cells get purged as stem cells along the way
- According to the atavistic model: cancer begins with a stem-like cell
- They’re already purged epigenetically closer to neoplasm
- You can see this in the methylation patterns, etc.
- Or they revert that pattern
- There are triggers: it could be a nuclear gene mutation, it could be mitochondrial damage, the disruption of the tissue architecture
- Then what happens is the cell reverts to the “safe mode”
- But it begins running the arrow of evolution backward, away from the modern genes of multicellular living and cooperation, and towards earliest genes, of early embryogenesis, of replicative immortality
- We’ve known this: cancer cells re-express fetal genes, they’re expressing these early genes of embryogenesis
Embryogenesis looks a lot like cancer:
- Highly glycolytic
- They exhibit replicative immortality
The re-expression of fetal genes is what’s defining cancer:
- Within a multicellular context, we’ve divested our immortality to the germline
- The methylation tags, epigenetic signals get wiped clean every time we go through embryogenesis, and that’s what’s happening with cancer
- Global hypermethylation
- Hypermethylation of the promoter regions of tumor suppressor genes
Human embryonic genes re-expressed in cancer cells
Human preimplantation embryonic cells are similar in phenotype to cancer cells. Both types of cell undergo deprogramming to a proliferative stem cell state and become potentially immortal and invasive (Monk and Holding, 2001).
The most important effector of cancer’s metabolic phenotype is the transition from hexokinase 1 to hexokinase 2
Hexokinase 2 is required for tumor initiation and maintenance and its systemic deletion is therapeutic in mouse models of cancer (Cancer Cell;24,2,213-228,2013TK)
- The first enzyme of glycolysis is HK1
- A little in skeletal muscle and heart
- Cancer transitions to HK2, and then it wildly overexpresses it
- HK2 is less subject to product inhibition to glucose-6-phosphate
- Great for replicative immortality
- Responsible for the Warburg effect
- It binds to the VDAC channel
- Associated with outer mitochondrial membrane
- It induces a conformational change that closes the VDAC channel
- The VDAC channel is the effector pore for apoptosis
This one transition to an isozyme that’s preprogrammed in us is responsible for two hallmark features of cancer
- Warburg effect
- Immortalization of the cell
Hexokinase 2 is responsible for the Warburg effect and immortalization of the cell
- Most people attribute a PET scan to overconsumption of glucose (true)
- More because HK2 phosphorylates glucose which is an irreversible reaction, which bloats the cancer cell
- You wouldn’t have a PET scan without HK2
Developmental profile and regulation of the glycolytic enzyme hexokinase 2 in normal brain and glioblastoma multiforme
Paper in Neurobiol Dis (Wolf et al., 2011 CKTK)
“HK2 expression was highest in the early embryo, while HK1 expression increased with CNS maturation.”
- Is there any other time that HK2 is overexpressed other than cancer?
- Very early on during embryogenesis
- A good theory has predictive power: this is exactly what you would expect
Cancer is “hop-scotching back in time to the Proterozoic ocean
- The earth’s atmosphere had dramatically less oxygen, when unicellular life evolved
- Glycolysis is the most ancient and conserved biochemical pathway
- The degree of HK2 overexpression correlates to the degree of aggressiveness
The idea of an atavistic model:
- If the foundation of embryogenesis is that built-in pattern of replicative immortality, you can’t rid of it
- Evolution would get rid of cancer if it could, but it can’t because it’s the building block of embryogenesis
- The cancer cell is reverting back to this: it’s hop-scotching back in time
- During the great oxygenation of the planet is when multicellular life took over
“Geochemical data (1-6TK) suggest that oxygenation proceeded in two broad steps near the beginning and end of the Proterozoic eon (2,500 to 542 million years ago) (Tracing the stepwise oxygenation of the Proterozoic ocean, Nature, 452, 456-459, 2008 CKTK).”
You can see the exact methylation patterns that result in the overexpression of HK2:
Thus, bisulfite methylation footprint analysis revealed 18 methylated CpG sites within a CpG island (-350 to +781 bp) in the hepatocyte HK2 gene, but none in the hepatoma (Hexokinase II: Cancer’s double-edged sword acting as both facilitator and gatekeeper of malignancy when bound to mitochondria (Mathupala, Ko, and Pedersen, 2006 TK)
Therapeutic strategy of cancer 2.0
- We have to know what cancer is in order to treat it
- New theories guide cancer treatment strategy to epigenetic therapies: exploit differences in expression and/or engage the cancer cell in diplomacy — experiments have shown this is possible
- Direct and indirect epigenetic strategies
- DNMT inhibitors
- HDAC inhibitors
- Packaged microRNA (miRNA)
- Decoupling from adaptive immune system
- Ketogenic diet and HBOT
- Somatic mutations are not the whole picture
- Cancer is a systematic, organized disease of altered protein expression (e.g., HKII)
- This completely reconfigures therapeutic strategy away from the single cell hypotheses to diplomacy and the targeted killing of cancer cells
Tripping over the Truth
Chapter 3: Breakthroughs and Disappointments
Into the Dustbin of History
Though an iconic member of one of science’s most decorated fraternities in a golden era of science, Warburg had his theory on the origin of cancer slain and buried. Weinhouse put the final nail in the coffin the same year that Varmus and Bishop established mutations to DNA as the singular and undisputed origin of cancer. Warburg’s theory joined the list of disproven theories, ideas that grew like branches from the tree of knowledge only to die and fall off.
Five years after Weinhouse’s scathing review, in 1981, Hans Krebs, Warburg’s former student, friend, and fellow Nobel laureate, wrote a biography of Warburg titled Otto Warburg: Cell Physiologist, Biochemist, and Eccentric, so that his spectacular career would not be forgotten. Even to Krebs, for Warburg, cancer research may have been the only blemish on what was an otherwise outstanding career. Krebs wrote this of the speech Warburg gave at the Lindau meeting four years before his death:
He still showed a clear, logical, and forceful style but the balance of his judgment, in the view of most experts, is at fault. His sweeping generalizations spring from gross simplification. The partial replacement of respiration by glycolysis is only one of many characteristics which distinguish cancer cells from normal cells. Warburg neglected the fundamental biochemical aspect of the cancer problem, that of the mechanisms which are responsible for the controlled growth of normal cells and which are lost or disturbed in the cancer cell. No doubt, the differences in energy metabolism discovered by Warburg are important, but however important; they are at the level of the biochemical organization of the cell, not deep enough to touch the heart of the cancer problem, the uncontrolled growth. Warburg’s “primary cause of cancer”—may be a symptom of the primary cause, but is not the primary cause itself. The primary cause is to be expected at the level of the control of the gene expression, the minutiae of which are unknown though some of the principals involved are understood.
A Flickering Ember
Warburg was able to grossly describe what he believed to be the fundamental alteration in cancer cells: they fermented glucose in the presence of oxygen. But Warburg failed to discover why or how cancer cells exhibited the Warburg effect. After Varmus and Bishop’s discovery of the cellular origin of viral oncogenes in 1976—and with Warburg thoroughly discredited—it was not an exaggeration to say that no one except Pete Pedersen of Johns Hopkins considered the metabolism to be at the “heart” of the cancer problem. The work he did while nobody was paying attention served as scaffolding for future researchers to climb as decades passed and they begin to realize that the metabolism of cancer held a missing piece to a puzzle that genetics had not been able to solve.
BK: The Why of cancer cells exhibiting the Warburg effect?
Having established the reason that cancer cells must generate energy by fermentation (to compensate for their missing and damaged mitochondria), Pedersen set out to discover how cancer cells ramped up fermentation. The missing and damaged mitochondria were the why of the Warburg effect. Pedersen wanted to discover the how of the Warburg effect.
BK The How of cancer cells exhibiting the Warburg effect?
…Rather than retaining a healthy cell’s exquisite ability to regulate the amount of glucose entering the fermentation pathway, the valves of the cancer cell that regulated the flow were stuck open. The protein that catalyzed the first step of glycolysis (converting glucose into glucose-6-phosphate by tagging it with a phosphate group) is called hexokinase, and it alone determined the how of the Warburg effect. The how is the result of molecular square dance. The behavior of the cancer cell is drastically altered as one form of hexokinase “do-se-doed” into a slightly different form of hexokinase [HK2], dramatically altering the way the cell behaved. The “cancerous” version of hexokinase is a vestige of the past, the result of the evolutionary process as it moved through time.
“When you come to a place like Hopkins, and you have to compete with all these brilliant people, I realized I was way ahead of them, not because I was smarter, but because I could out work all of them,” he said.
The timing was perfect. He went to work for the famous biochemist Albert Lehninger, a giant in the field of energy metabolism. In 1948, along with his student Eugene Kennedy, Lehninger discovered that mitochondria were the site of the cells’ energy production, igniting an explosion in the understanding of cellular energetics. “Lehninger was a wonderful mentor,” said Pedersen. “He often spoke of Warburg and knew Warburg personally.” The serendipitous collision with the leading biochemist and his connection to Warburg created the perfect atmosphere for a young biochemist interested in cancer. Pedersen said, “It was like a passing of the baton, from Warburg to me, through Lehninger.”
But the era of great biochemists, especially those studying cancer, was essentially over. If Pedersen was to continue the line, he would have to go it alone. When Lehninger died in 1986, Pedersen was one of the final links to Warburg. He was left as one of the few shouldering the notion that the answer to cancer lay in metabolism.
Nevertheless, he soldiered on. His persistence led to a series of important discoveries that coalesced into a larger image, one in which Warburg had painted the first brush stroke. Warburg pinned the origin of cancer on “injured respiration,” but he lacked the experimental technology to closely study the mitochondria of cancer cells, structures he called grana. With the help of his mentor, Lehninger, and emerging technologies, Pedersen was able to look directly at the mitochondria of the cancer cell and set off to determine if, as Warburg guessed, they were dysfunctional.
Shortly after arriving at Johns Hopkins, Pedersen read about a researcher who had developed strains of rats harboring cancerous tumors that grew at different rates. This sparked his interest. “Some would grow very fast, killing the animal in a matter of weeks. Others would grow very slowly, taking almost a year to kill the animals. And others were in the middle,” he said. The different rates of tumor growth raised an important question. What metabolic difference caused some to grow slowly and others to grow fast? The rats were developed by Harold Morris at NCI, a short drive from Johns Hopkins. Pedersen and a technician, Joanne Hullihen, drove to NCI to meet Morris and his rats. “He was a nice guy, he gave us a number of his rats to work with.” Pedersen and Hullihen loaded up the rats and drove back to Johns Hopkins.
Back in his lab Pedersen began investigating the biochemistry of the rat’s tumors, and he discovered a powerful correlation. Critically, the faster a tumor grew, and the more aggressive it was—the lower the overall number of mitochondria, and the more it fermented glucose. He thought this counterintuitive fact revealed something fundamental about the nature of the cancer cell. He knew this correlation couldn’t exist in a vacuum, and it had to have some significance. “That’s when I began to go back and reinvestigate all this business about Warburg.”
He began compiling evidence showing how injured the cancer cell’s ability to respire was. Simply counting the number of mitochondria compared to normal cells provided direct evidence. Numbers alone revealed that the cancer cells had a reduced ability to respire. In every experiment, he counted the same thing: the tumor cells that exhibited a robust “Warburg effect” and grew the fastest invariably retained about 50 percent of the mitochondria compared to normal tissue-matched cells.
TK Where did the other 50% of mitochondria go?
Here was a quantitative explanation for Warburg’s hypothesis that cancer stemmed from insufficient respiration. It was no longer a guess, the numbers proved it.
As Pedersen dug deeper, he found that the mitochondria from cancer cells that grew the fastest were rife with a spectrum of structural abnormalities. They were smaller, less robust, cup shaped, dumbbell shaped, missing important internal membranes, and had numerous abnormalities in their protein and lipid content. Again, in biology, structure equaled function. Pedersen irrefutably showed that the mitochondria of cancer cells were structurally altered almost everywhere he looked.
By 1978, he had a compiled a massive collection of evidence showing the extent of the deficiency and/or damage to the mitochondria, and by extension, to the respiratory capacity of the cancer cell. He was resurrecting Warburg’s discarded theory, but it was only two years after Varmus and Bishop sent cancer researchers off hunting oncogenes.
Nobody cared about Warburg’s stodgy theory, but Pedersen never questioned himself. “I knew I was right; the data didn’t lie.” Nevertheless, he couldn’t help but be perplexed by the degree of disinterest.
In 1978, he decided that it was time to publish his findings in a massive review of the cancer cell’s defective metabolism. He began the review with this question:
Despite the fact that mitochondria occupy 15–50 percent of the cytoplasmic volume of most animal cells and participate in more metabolic functions than any other organelle in the cell, it seems fair to state that cancer research, and consequently funding for it, has been directed away from mitochondrial studies in the past decade. The new student of cancer biology and biochemistry may ask “Why?”
With markedly reduced numbers and structurally distorted mitochondria, there appeared no way that cancer cells could generate sufficient energy to survive through respiration alone as Weinhouse had said they could.
Having established the reason that cancer cells must generate energy by fermentation (to compensate for their missing and damaged mitochondria), Pedersen set out to discover how cancer cells ramped up fermentation. The missing and damaged mitochondria were the why of the Warburg effect. Pedersen wanted to discover the how of the Warburg effect.
In 1977, seven years after Warburg’s death, Pedersen and a South American graduate student, Ernesto Bustamante, made a profound discovery. They discovered the single molecular alteration in the cell responsible for the increased fermentation that Warburg measured. The mundane title of the paper, “High Aerobic Glycolysis of Rat Hepatoma Cells in Culture: Role of Mitochondrial Hexokinase,” eclipsed the vast implications of its content.
“That was an important finding,” the perpetually understated Pedersen said. The discovery showed why the “gas pedal” controlling fermentation was stuck to the floor in cancer cells. Perhaps more importantly, it represented a pivotal therapeutic target that was present in virtually all cancers.
Some common themes are pervasive to all forms of life. Just like all forms of life use DNA as a blueprint of instructive code, life uses a single molecule, adenosine triphosphate (ATP) as a universal carrier of metabolic energy. ATP is used in the same way that money is used as a common intermediary for transactions within an economy. ATP is the common currency of energy. The energy carried within ATP lay in a single, high-energy phosphate bond located at the end of a string of three phosphates dangling from the center. The energy released from the cleaving of this single bond is captured and redirected, facilitating movement and the myriad unseen chemical reactions that cells continuously engage in. (As you move your eyes along the words of this sentence, ATP is spent to pull one muscle fiber along another, like a person pulling a rope, allowing your eyes to move from one word to the next.)
ATP is generated by the cell in two pathways: fermentation (glycolysis) or respiration (aerobic mitochondrial energy generation with oxygen). Glycolysis starts with one molecule of glucose, and through a series of ten steps, transforms it into two molecules of pyruvate.
Once pyruvate is generated, the cell has a decision to make. It can take pyruvate and shuttle it into the mitochondria, where it will begin the respiratory energy cycle – the highly efficient process that employs oxygen to generate a staggering twenty-three molecules of ATP. Alternately, the cell can ferment pyruvate, an inefficient method of energy production that produces only two molecules of ATP and generates a waste product, lactic acid.
A healthy cell could convert pyruvate to lactic acid for a good reason; a cancer cell could do the same for a bad one.
To illustrate why a healthy cell might ferment sugar, consider a scenario. Say you were hiking in the wilderness, and you encountered a bear. Without thinking, you took off running as fast as you could. Your muscles demanded prodigious quantities of ATP, depleting the energetic currency quickly. As you ran, you began breathing rapidly, saturating the cells with oxygen, driving ATP production through aerobic respiration in the mitochondria to maximum capacity. But your extraordinarily high energy demands required more than the mitochondria could give through aerobic respiration alone. Although extremely efficient, the aerobic machinery is unable to adjust rapidly and generate ATP in a quick, short burst. Your mitochondria were using as much pyruvate as they possibly could, so to generate more ATP, your cells were forced to convert the excess pyruvate into lactic acid allowing sugar to continue the rapid but more inefficient pathway of fermentation. The valves opened as wide as possible, and a waterfall of glucose entered the fermentation pathway, generating a quick burst of ATP. But it came at a price. Your legs began to burn as the lactic acid built within the muscle cells. You made it to your car just in time, having spent all of your energetic reserves. As you calmed down, the valves that regulate the flow of glucose through the fermentation pathway returned to a position that allowed a steady state of glucose to enter the system, producing no more lactic acid, and just enough pyruvate to enter the respiratory cycle to meet the needs of the cell. Your cells are remarkable self-regulating chemical engines that constantly adjust for maximum economy.
TK so does a cancer cell, but it has fewer, and more deficient, mitochondria, therefore more fermentation to compensate
As Bustamante and Pedersen discovered, rather than retaining a healthy cell’s exquisite ability to regulate the amount of glucose entering the fermentation pathway, the valves of the cancer cell that regulated the flow were stuck open. The protein that catalyzed the first step of glycolysis (converting glucose into glucose-6-phosphate by tagging it with a phosphate group) is called hexokinase, and it alone determined the how of the Warburg effect. The how is the result of molecular square dance. The behavior of the cancer cell is drastically altered as one form of hexokinase “do-se-doed” into a slightly different form of hexokinase [HK2], dramatically altering the way the cell behaved. The “cancerous” version of hexokinase is a vestige of the past, the result of the evolutionary process as it moved through time. To understand where it came from or how it came into existence, we have to briefly explore the dynamics of DNA as it moved through time and space.
Evolution came up with a fascinating method to fine-tune metabolism. The body needed new material to work with, and like all things Darwinian, it started with an accident. Where there was one hexokinase gene before, suddenly, through a random process called duplication, a person was born with two copies. Essentially, nature laid out a fresh canvas for evolution to act on. Over time, as the new copy was inherited from generation to generation, mutations (variations in the nucleotide sequence) accumulated until a mutation resulted in a protein with a slightly altered function that helped the cell. This was Darwin’s process of natural selection in a nutshell, the testing of new code in a given environment. The new gene, a slightly altered copy of an existing gene but with new functionality, is called an isozyme. Isozymes are like tires. They all serve the same function but have differences that make them better under certain conditions (such as snow tires versus street tires or mud tires). Within our DNA, hexokinase exists as four different isozymes. Each catalyzes the first step of fermentation, but each is specialized for a given purpose within a given cell.
When Pedersen and a postdoctoral fellow, Richard Nakashima, peered inside the cancer cell, they noticed a drastic alteration in the way hexokinase was normally expressed. First, the cancer cell switched from its normal isoform of hexokinase to a rare form called hexokinase II. Second, the cells were producing vastly more of it. This singular molecular detail, he reasoned, could be the how behind the Warburg effect.
Normal hexokinase is self-regulating (just as the way a full stomach sent an “I’m full” signal to the brain). As the product of the hexokinase reaction, glucose-6-phosphate, built up, it signals hexokinase to slow down; this is called product inhibition. The irreverent form of hexokinase, hexokinase II, ignores the signal to slow down and keeps the valve wide open, shoving as much glucose as it can down the fermentation pathway.
In addition to the embezzlement of the body’s energetic reserves, Pedersen envisions another consequence from hexokinase II’s proclivity to force glucose down the cell’s throat. “Lactic acid may build up, damaging surrounding normal tissue, helping pave the way for invasion and metastasis.”
The normal regulatory mechanisms of the cell, as Pedersen and his students discovered, was subverted in the cancer cell, producing massive quantities of a perverted enzyme and slamming the fermentation pathway’s “gas pedal” to the floor.
Why would evolutionary pressures select for such a malevolent form of a normal enzyme? Hexokinase II must have provided the cell some sort of advantage in our evolutionary past. It could be as simple as allowing the prebiotic cell to survive periodic episodes of hypoxia, when a cell found itself in an environment with little oxygen. It was a “nursemaid” version of an enzyme, there to pull the cell through the difficult moments that undoubtedly occurred across our tenure on the planet. Today, hexokinase II might be the enzymatic version of the appendix—a body part that served a function at one time, but no longer does. As the outdated remnant was dragged through time, it transformed into something else, something malicious. The evolutionary process that created the component had yet to slough it off, leaving it hanging in the wind, allowing it to fester and decay.
Even if the cancer research community at large, with its myopic focus on DNA, ignored Pedersen and his students’ discovery of hexokinase II, somebody was paying attention. A serendipitous melding of Pedersen’s discovery with an emerging technology led to one of the most important breakthroughs in cancer diagnostics, one that has likely helped save untold numbers of lives.
BKTK ideas + energy + equipment + (wasting) time
The PET Scan
In the 1970s, the nascent technology of positron-emission tomography (PET) scanning was floundering. The problem was not with the detectors, the problem was finding something worth detecting. Those seeking utility for the device needed a compound that not only the detector could see but one that concentrated itself at the site of diseased tissue, allowing for contrast between normal tissue and diseased tissue. The answer came from Pedersen’s lab’s discovery of the cancer cell’s conversion to and overexpression of hexokinase II.
Once hexokinase II “tagged” glucose with a phosphate molecule, it was trapped inside the cancer cell. The hyperactivity and overexpression of hexokinase II resulted in cancer cells that were bloated with glucose. Here was the contrast between normal and diseased tissue needed for the diagnostic application of a PET scan. All that was then needed was a form of labeled glucose that the detectors could pick up, and it came shortly in the form of fluorodeoxyglucose (FDG), a molecule that looked like glucose but had a single oxygen atom replaced by an isotope of fluorine. This was an atom that would provide a signal.
Pedersen recalled a link between his discovery of hexokinase II and the development of PET scanning. “In the late 1970s, I was invited to give a seminar on hexokinase II at the NIH. And this man named Giovanni Di Chiro was in the audience, he was in a wheelchair, and he was very interested in what I was talking about—and then the use of FDG to detect cancer in PET scans came shortly after. I can’t draw a direct line between my discovery of hexokinase II and the PET scan, but one way or the other the discovery of hexokinase II led to it.”
PET scanning revolutionized cancer diagnostics. To this day, no imaging technology is able to differentiate living, actively metabolizing cancer with the accuracy of the PET scan. “CT scans can image a spot, but they can’t tell you if the cancer is alive or dead. PET scans are the only way to detect actively metabolizing tumors,” Pedersen said.
Soon after its development, the technology made its way into virtually every cancer center across the globe, allowing for the diagnosis and tracking of untold numbers of cancer patients. After fasting for six hours, a patient undergoing a PET scan is injected with FDG and told to lie still so that the glucose-like compound isn’t taken up by muscle, creating artifacts that confuse the image. For an hour, the patient lies quietly while the glucose-analog diffuses through the body. Because of hexokinase II, the labeled glucose begins to concentrate inside cancer cells. After an hour has passed, when the patient is exposed to the detector, an elegant cascade of subatomic reactions occurs. A positron emitted from the fluorine atom collides with a nearby electron, annihilating both, but in the process, emitting a gamma ray that is converted to a photon (light). The detector then casts forth bright spots that illuminate the source: the tumor.
The process of a PET scan was a dramatic visualization of cancer’s grotesquely voracious appetite for glucose. The scan was evidence of cancer’s perverted metabolism, the Warburg effect, and Pedersen’s unruly enzyme hexokinase II. Oncologists all over the globe read millions of PET scans, staring at the quality that Warburg and Pedersen had claimed defined cancer. Ironically, Pedersen, the star researcher who was largely ignored, inadvertently, together with his students, provided the cancer community with a tangible, visual target that could be exploited. They had been staring at it every day.
A New Era
Meanwhile, as Pedersen carried Warburg’s baton, the first realization of the promised targeted drugs was about to come to fruition. It was the first step away from the indiscriminate first generation of chemotherapy and toward a modern, rational era that promised to be more effective and less toxic.
In contrast to the wall of silence that greeted Pedersen’s work, the first targeted drug, Herceptin, was carried to term in a charged environment of worldwide anticipation. Herceptin carried the weight of Atlas. It was saddled with soaring expectation—it was a drug of the future, the first product of purely rational drug design. The path from idea to FDA approval contained all the drama and vicissitudes of a Hollywood production: heroes, villains, rich philanthropists, impassioned activists, desperate cancer patients, and stoic visionaries. In the end the story was told in television shows, newspapers, and books, and it was even made into a movie.
With the discovery that cancer originated by mutations to proto-oncogenes, the map to targeted drugs was established. Critical “driver” oncogenes had to be identified. That was the easy step. Figuring out the structure and function of the oncogenes’ protein products would be more difficult, and the next step, designing drugs to target the dysfunctional proteins, would be even harder yet. But the inherent logic of the process was laid out, despite the obstacles it might contain. The path to drugs was clear. Scientists knew what they had to do.
During the 1980s, Weinberg was perhaps the scientist most efficient at identifying oncogenes. He was so good at finding oncogenes that he had achieved no small measure of fame (one author described the fame Weinberg achieved, “in the People magazine definition of the word”). Though he had yet to win a Nobel Prize, he was “as lavishly decorated as the joint chiefs of staff.” His combination of popular and vocational fame meant that he was the “guy industry turned to when they felt flush and philanthropic.”
In 1982, Weinberg’s laboratory discovered another oncogene that was isolated from rats bearing a tumor called a neuroblastoma—the lab called the oncogene “neu.” Neu had a quality that distinguished it from other oncogenes: it possessed traits that made it the perfect target for rational, targeted drug design. Most of the oncogene products discovered in Weinberg’s lab coded for proteins that were isolated to the cytoplasm of the cell, the vitreous fluid filling the interior of the cell. With most of the oncogenic targets comfortably protected in the cell, the scope of possible drug candidates was compressed to those able to breach the cell’s membrane barrier before seeking out the target—not a trivial task. But neu was different. The gene neu transcribed a protein that was designated to become a receptor on the outside of the cell. The receptor received a signal when a specific growth factor docked onto it, the receptor then relayed the signal to the nucleus, telling the cell to divide. From a drug design perspective, neu’s accessibility was key. It was low-hanging fruit, positioned so that drugs had easy access to it.
Months after the discovery of neu, Weinberg published his finding, but incredibly, neu’s potential as a drug target was left out. Somehow, its therapeutic potential escaped Weinberg and the others in his lab. With so many new oncogenes being discovered and so many pieces to connect, his attention was miles away in the theoretical clouds of cutting-edge cancer theory. “We just missed it,” Weinberg said when speaking of neu’s potential as a drugable target. For the time being, its potential was left hanging. But not for long.
Soon the human version of neu was discovered in an entirely different context: under the ceiling of a profit-driven pharmaceutical company. This time the utilitarian nature of neu was not missed, because it was the impetus behind the search in the first place. The human version of neu resembled another known gene, the epithelial growth factor receptor. This was an antenna-like molecule sitting on the surface of the cell that, like neu, when stimulated by its hormonal counterpart, sent a signal to the nucleus to divide. The new oncogene was called human epithelial receptor (Her-2). (It is now referred to as Her-2/neu, acknowledging its codiscovery.) The context of its rediscovery, from the theoretical ambiance of an academic lab to that of a goal-oriented company that had to answer to shareholders, drastically altered its trajectory.
By the late 1970s, the revolution in molecular biology had spun out a new breed of pharmaceutical company dedicated to capitalizing on the promise of targeted cancer therapy. It was a stark departure from the typical pharmaceutical companies that sold everything from Band-Aids to baby food. A new generation of companies with laser-like focus began to pop up on the coasts next to cutting-edge universities.
South San Francisco’s Genentech was one such company. Drawing from the innovative culture of the Bay Area, talent moved seamlessly from the halls of the university to the halls of Genentech. Even Genentech’s conception was unique. The company didn’t start with the discovery of a drug. It started with a process, or a technology to make drugs and an infusion of venture capital. The name, Genentech, was derived from Genetic Engineering Technology, an exciting technology discovered in the late 1970s, used to “cut and paste” almost any gene into the genome of bacteria cells, thereby transforming them into factories capable of churning out prodigious amounts of the desired protein. Before Genentech, drugs like insulin were obtained by the clumsy and inefficient process of extraction from cow and pig guts. It was so inefficient that it took eight thousand pounds of ground pancreases to extract a single pound of insulin. After Genentech, the human insulin gene was spliced into bacterial cells, subverting them into remarkably efficient insulin-producing machines—a much cleaner and streamlined manufacturing method.
A decade after its inception, Genentech found itself in an uncomfortable position. It had revolutionized the process of manufacturing protein drugs, but after ten years of dazzling growth, drugs to manufacture ran out. The company had three blockbusters to its name: insulin for diabetics, a clotting factor for hemophilia, and growth hormone for a variety of childhood growth problems. Genentech was fantastic at one aspect of pharmaceutical development, but it was not in the tricky, high-risk, high-reward business of developing new drugs – at least not until the company ran out of proteins to manufacture. To design a new drug, first a target was needed, something Genentech was not accustomed to searching for. To stay relevant, the company had to shift focus. Again tapping the innovative talent in the Bay Area, the company launched a department dedicated to discovering drug targets.
German-born Axel Ullrich, a passionate scientist with a rugged charm enhanced by a German accent, was assigned to find drug targets. He was trained as a postdoc at the University of San Francisco, and the supercharged atmosphere that enveloped the Bay Area in the late seventies and eighties infected him. Varmus and Bishop were just down the hall. Ullrich’s transition from academia to pharmaceutical company particularly suited his can-do nature and the culture at Genetech made the move easy. Genentech retained the free-flowing, uninhibited atmosphere of academia, scientists were largely given free reign.
When Ullrich began his search for oncogenes to target, he had a head start. He had already isolated and cloned a mutated form of a growth receptor thought to be responsible for causing blood cancer in chickens. In the world of molecular cancer biology, this was a breakthrough. For the first time, a connection between a mutated growth receptor and cancer was made, linking cause to effect. Using this example Ullrich began to look for a growth receptor responsible for cancer in humans. His search paid off when he teased out Her-2, the homolog of Weinberg’s oncogene neu. Unlike Weinberg, Ullrich recognized the potential of his discovery. It was a clear oncogene and it was a sitting-duck, the longimagined fantasy of rational drug design. Ullrich had his target, but he had more obstacles to overcome. He would have to see what types of cancer Her-2 was active in, and then he would have to design a drug that blocked the Her-2 receptor. The process from target to drug was propelled by a series of fortuitous events. Puzzled by the first problem— how to determine which cancers were driven by Her-2—an answer came from a chance meeting in the Denver Airport.
Ullrich was on his way home after presenting a seminar on Her-2 at the University of California Los Angeles (UCLA). Dennis Slamon, an oncologist with a PhD in cell biology and a self-reported “murderous” obsession for curing cancer, was also at the airport, waiting for his plane. Slamon had just attended Ullrich’s lecture in LA, and as he waited, he mulled over a solution to Ullrich’s problem of which cancers Her-2 was active in. The scientists struck up a conversation. Ullrich had the oncogene, but he didn’t have the tissue samples to test it with. Slamon did. His compulsion to cure cancer included a healthy obsession. He collected samples of tumors of all kinds, saved in a freezer, for no other reason than he felt they might prove useful someday.
Over drinks, they plotted their course. Ullrich would send Slamon DNA probes for Her-2. Slamon would then test his samples to determine which ones, if any, expressed the product of the oncogene, answering the question of which cancers were driven by Her-2. Ullrich described the events that led to Herceptin as “an amazing amount of luck.”
Once home, Slamon got to work. After exhaustively probing his samples, he called Ullrich. “We’ve got a hit,” he said. Ullrich’s probe had found its target, Her-2, in some of Slamon’s breast and ovarian cancer samples. The next step was to determine what Her-2 was doing in the samples, how it was causing cancer. Typically, oncogenes were mutated versions of normal genes, resulting in defective protein products, but Her-2 operated by a different mechanism. It amplified itself by duplicating itself over and over again, like a copy machine with its “copy” button stuck. It transformed normal cells into cancerous ones by “overexpression.” A normal breast cell might contain fifty thousand Her-2 receptors on the surface of the cell. The breast cancer cells that “lit up” Ullrich’s probe contained up to 1.5 million receptors.
Her-2 wasn’t mildly overexpressed on the cancer cells, it was grotesquely overexpressed. The result was cells that were hideously hypersensitive to the presence of growth factors—cells primed to misinterpret a normal signal to divide. But not all Slamon’s breast and ovarian samples contained the amplified Her-2 gene. Only about one in five did, and this allowed him to categorize breast cancer into two camps: Her-2 positive and Her-2 negative. All the evidence pointed to Her-2 being a legitimate transforming oncogene, but with the stakes so high—it took more than $100 million to bring a drug to market—the research pair had to be sure.
Mutations within the DNA of cancer cells could be divided into two groups: drivers and passengers. Alterations of designated drivers did what the name suggested: they drove cancer. Passengers, on the other hand, didn’t transform a cell but were only along for the ride. Ullrich and Slamon had to make sure that Her-2 was a driver and not a passenger. Slamon was in the position to make the determination, by observing whether there was a difference clinically between Her-2 positive and Her-2 negative cases of breast cancer. Carefully following patients in both camps revealed something remarkable: Her- 2 positive cases resulted in a more aggressive and virulent form of cancer with a worse prognosis, exactly what would be expected if Her-2 was a driver. Ullrich performed another experiment to test the capacity of Her-2 to act as a driver. He sprinkled the Her-2 gene over normal cells and manipulated them into taking up the new gene and incorporating it into their DNA. This resulted in the same overexpression observed in the breast cancer samples. Subverted by the overexpression of Her-2, the cells ignored the intricate signals of controlled cellular division and turned into crazed proliferators. Her-2 alone marched the cells down the path to malignancy. It seemed as though Ullrich and Salmon had the target Varmus and Bishop had promised. Now all they needed was a bullet.
The creative revolution occurring in molecular biology resulted in another profound breakthrough that harnessed the remarkable qualities of the immune system. The immune system is the only barrier between us and the relentless assault of the microbial world. It is a battle-hardened collaboration of specialized cells honed through millions of years of all-out war. The immune system’s ability to selectively attack foreign invaders with specificity left immunologists in awe. Nature’s version of “drug design” made our attempts look silly. The immune system is a sophisticated cellular militia that contains all the elements of a modern military. Cells called macrophages act like tanks. Wielding an imposing armament of weapons, they chase down enemies and unleash vicious assaults. Commander cells direct the battle, calling forth troops and orchestrating flanks, surprise attacks, and a gamut of brilliant maneuvers, honed through eons of experience. The immune system also comes equipped with targeting missiles called antibodies. They are fired from the outer membranes of specialized cells called b-cells that display an inconceivably vast armament, able to target almost every virus and bacteria on the planet. In the midst of an infectious assault an activated b-cell turns into a biological machinegun, churning out approximately 2000 antibodies per second. It was the antibodies that caught the attention of researchers—specifically, their ability to target any conceivable invader. To researchers trying to develop drugs, they were long sought after “magic bullets.”
The idea of targeted drugs captured the imagination of biologists as far back as 1908 when German scientist Paul Ehrlich popularized the concept of a “magic bullet.”
TK methylene blue Paul Ehrlich PeopleTK
He imagined a compound designed to selectively target disease-causing organisms. His inspired vision of medicine became reality in the late twentieth century when rather than trying to engineer targeted drugs themselves, researchers employed the immune system to do it for them. They found that they could coax antibody-producing cells (b-cells) to do their bidding. They injected a mouse with the desired target, causing the immune system of the mouse to scale up the b-cells armed with the antibody targeted to the foreign substance. They then isolated the b-cells from the spleen of the mouse and fused them with a cancerous myeloma cell in a sort of arranged marriage. They capitalized on the cancer cell’s hyperactive growth, harnessing its perversion for utility. The hybrid cells were transformed into factories that churned out prodigious amounts of an antibody that could be targeted to virtually anything. Once manufactured, isolated, and purified, the antibodies were called monoclonal antibodies. Here was the magic bullet they needed.
Ullrich requested something from the experienced immunology department at Genentech: a monoclonal antibody targeted to the Her-2 protein. With the magic bullet soon in hand, he performed one more simple experiment. In a petri dish, he treated Her-2 positive breast cancer cells with the monoclonal antibody. The antibodies performed their singular task with exquisite precision. They honed in on the Her-2 receptor, binding to it, covering its surface like a tarp, and blocking its ability to receive any signal to grow from the outside. The antibody brought the growth of the cancer cells to a screeching halt. When Ullrich washed the antibody from the surface of the cell, the growth resumed like nothing had happened, unequivocally proving the antibody’s efficacy and mechanism of action. When recalling the simplicity and powerful implications of the experiment, Slamon said, “It was fantastic.”
Ullrich and Slamon had all the proof they needed, but they had the formidable task of convincing the top brass at Genentech to gamble $100 million on their idea, a task that proved to be Ullrich’s undoing. Unable to convince management of the potential of their concept, Ullrich became increasingly frustrated. His disenchantment spiraled until he quit and moved to other academic and commercial pursuits.
Raised by an Appalachian coal miner, Slamon retained the stubborn, gritty determination that flowed through the veins of humble, bootstrapping families. Unlike Ullrich, Slamon dug in and was going to see the endeavor to the end no matter what. He was about to be on the receiving end of some remarkably good luck.
In 1982, Slamon was a red-faced, junior attending physician treating a man with recurring Hodgkin’s disease. Like every other type of cancer, Hodgkin’s carried a much worse prognosis upon reoccurrence. The patient was Brandon Tartikoff. He was thirty years old and NBC’s new “golden boy of programming.” Tartikoff either conceived of or championed hits like The Cosby Show, The Golden Girls, Miami Vice, Cheers, and Seinfeld, and he put NBC on top of the ratings.
Tartikoff’s treatment included nine cycles of chemotherapy over the course of one year. In that time, remarkably, he transformed NBC and fathered a child, all in the midst of a chemotherapeutic-induced fog. The struggle caused the Tartikoffs and Slamon to grow close; even their kids became friends.
In 1986, four years after the chemo had ended and Tartikoff’s two-year checkup came back clear, his wife, Lilly, wanted to do something for Slamon. She felt that Slamon had saved her husband’s life, and she wanted to pay him back by donating to his research. Slamon insisted that her only obligation was to pay the bills. Every time Lilly tried to donate to Slamon’s research, he refused. This went on for two years – Lilly trying to settle her perceived debt, and Slamon refusing. In 1989, Lilly wouldn’t take no for an answer. “I don’t like to owe anybody anything,” Lilly said. “He saved Brandon’s life, and this was payback.” She called Slamon. “I’m sick of this no, no, no. I’m going to do something for cancer, I’m not just doing it for you.”
Her persistence wore Slamon down. When he finally agreed, Lilly began a money-raising crusade. She solicited her billionaire friend Ron Perelman, the owner of Max Factor and Revlon. “You’re making all this money from women, and you should give some back,” she told him. Her persistence eventually convinced Perelman. He wrote a check for $2.5 million for Slamon’s research. Overnight, Slamon became the best funded researcher at UCLA.
The infighting about Herceptin continued at Genentech. The biotech company was reluctant make an “all in” bet on the drug. Slamon and his Revlon money (which ended up totaling more than $13 million from 1989 to 1997) resolved the issue. It provided the push that Genentech needed to tip the risk-reward ratio in its favor. “Without Denny Slamon and his Revlon money, there would be no Herceptin,” a Genentech executive said. With it, the world’s first targeted drug was born.
The amalgam of a cutting-edge biotechnology firm, Hollywood money, and the promise of a targeted cancer drug proved too seductive for the press to ignore. No cancer drug had ever been greeted with such fanfare. Well-known breast cancer specialist Craig Henderson described Herceptin as “the first step in the future,” away from the “poisons” of the past. The New York Times called it “a significant medical breakthrough” and said that Herceptin “opened a new frontier in cancer therapy.” Herceptin inspired people to quote Winston Churchill. “Now this is not the end. It is not even the beginning of the end. But it is perhaps the end of the beginning,” Dr. Mary-Claire King, the American Cancer Society professor of genetics wrote in the introduction of Robert Bazell’s book, HER-2: The Making of Herceptin, a Revolutionary Treatment for Breast Cancer. The platitudes were everywhere: “a whole new era of cancer treatment,” “groundbreaking,” and “revolutionary.”
In the spring of 1998, ASCO, the professional organization of cancer specialists, held its annual meeting at the downtown convention center in Los Angeles. Herceptin had completed its fitful journey through clinical trials. The glamorous, famous drug was ready for its unveiling. Typically the doctors shuffled from presentation to presentation, going through the motions, but on this Sunday afternoon, the vast majority, eighteen thousand strong, squeezed into an auditorium to hear Slamon give the results of Herceptin’s clinical trial. It was the marquee event.
A hushed silence greeted Slamon as he made his way to the podium. He began with the tumultuous history of the drug but couldn’t tell the entire story of what it took to get there, including the collective efforts of Pott, Hansemann, Rous, Varmus, and Bishop. The journey transcended generations of effort. The moment was the manifestation of the impeccable logic that guided Herceptin’s engineering from target to drug.
The adjectives describing Herceptin and all the pomp and ceremony were without meaning if the drug didn’t meaningfully impact breast cancer patients. Slamon paused before delivering the results. “Herceptin demonstrates a clear benefit in every conceivable index of response. Response rates compared to standard chemotherapy had increased by 150 percent. Herceptin shrunk half of the tumors in the women treated compared to a third in the control arm.”
Viewed from a different angle, Slamon’s words sounded different. Albeit a convenient way to make a drug sound better than it may be, tumor shrinkage is meaningless to those fighting for their lives. It was a sanitized method of measuring a response, a statistic scrubbed clean of anything meaningful. To say “150 percent” when describing the results of a drug sounded good, but the only issue that mattered was survival. It was not clear whether Slamon gave the unsanitized version of Herceptin’s results at the conference. If he did, it would have gone like this: “Herceptin is able to extend the life of a metastatic breast cancer patient by four months.” A decade later, a follow-up study revealed that adding Herceptin to standard chemotherapy was able to increase absolute differences in overall survival by 2.9 percent at four years, 5.5 percent at six years, 7.8 percent at eight years, and 8.8 percent at ten years. This was significant to the fraction of patients who fell into the percentage saved but maybe not worthy of the hyperbole showered on the drug.
Mark Twain said, “Facts are stubborn, but statistics are more pliable.”
Beyond the statistical sledgehammer—that the most-anticipated drug provided a marginal benefit in overall survival in maybe 15 to 20 percent of breast cancer cases—was an unspoken observation.
In Ullrich’s experiment, adding the Her-2 gene to normal cells turned them into cancer cells, establishing the fact that Her-2 alone could cause cancer. Other labs offered further proof that Her-2 could make a normal cell cancerous. Philip Leder at Harvard Medical School bred a strain of mice that overexpressed Her-2 from birth. The mice developed breast cancer at an unusually high rate. The tumors dissolved when treated with the antibody. Mike Shepard (who took over the Her-2/neu program when Ullrich resigned) described the process succinctly: the program was a blueprint for the proper biotech method. “First you understand the molecular events that give rise to a dangerous cancer. Then you look at that pathway, and based on technology that you have in your hands right now, you design in your head a treatment,” Shepard said. The overexpression of the Her-2 gene was the molecular event determined to cause or “drive” a certain subset of breast cancer. Herceptin smothered it and choked it off, neutralizing the event determined to be the cause, yet it was of marginal benefit. Something was clearly wrong.
If Herceptin was not a cure, or not translating into substantial benefit in life extension, something else was driving the cancer. The impeccable logic that guided the creation of Herceptin contained a fatal flaw. If the overexpression of Her-2 was the singular cause of a subset of cancer and Herceptin was the antidote, by extension, the women should be cured.
Nobody was talking about that after the ASCO meeting concluded and Herceptin’s unveiling was over. All those involved in creating Herceptin were there to celebrate. The drinks flowed freely. They did have a lot to celebrate, because the exhausting journey for the FDA approval of Herceptin was complete. Over the next ten years, the drug put almost $6.7 billion into Genentech’s coffers.
An Old Target Is New Again
During the late 1990s, as Herceptin dominated the headlines of oncology, behind the scenes, Pedersen was methodically elucidating cancer’s perverted metabolism. As far back as 1978, he had established that relative to normal cells, tumor cells had fewer mitochondria, and the ones he did find were terribly distorted, proving that tumor cells had a reduced capacity to produce energy aerobically. In 1977, his laboratory isolated the metabolic defect responsible for the Warburg effect: the hijacking of normal hexokinase by hexokinase II, followed by its monstrous overproduction. In 1986, his group and another group at the University of Maryland, headed by Marco Colombini, noticed that they were doing similar research and decided to collaborate. Together they showed that hexokinase II didn’t exist in isolation; it bound to another mitochondrial-bound protein called the voltage-dependent anion channel (VDAC). VDAC acts as a gateway for molecules (like ATP) to enter and leave mitochondria. Additionally, VDAC serves a functional role in the process known as apoptosis, “programmed cell death,” allowing the release of a trigger molecule, cytochrome c, which initiates a cascade of events that culminate in the death of the cell.
A variety of cellular insults trigger a cell to undergo apoptosis. It is a highly refined and organized process designed to remove damaged cells quickly and efficiently, maintaining the fidelity of the organism and preventing the buildup of excessive waste, which could result in disease. Apoptosis is a critical cellular process, the importance of which is often underappreciated, but it also requires an organism to strike a precarious balance. The balance between cell growth and cell death is a tightrope the body must walk everyday with billions of cells condemned to death through apoptosis and billions of cells dividing to replace them. If the tenuous relationship shifts too far toward cell death, degenerative conditions like Parkinson’s disease, Alzheimer’s disease, and Amyotrophic lateral sclerosis (ALS) can occur. If shifted too far toward growth, cancer may occur.
The laboratories of Pedersen and Colombini discovered that hexokinase II was binding with VDAC. When bound to Hexokinase II VDAC locked the gate, preventing the release of cytochrome c therby preventing apoptosis and effectively immortalizing the cell – one of the most salient and awe-inspiring qualities of the cancer cell. However, unlike the overexpression of the oncogene Her-2/neu, which occurred in only a fraction of cases of breast cancer, the overexpression of hexokinase II occurred in virtually every cancer cell. In one fell swoop, the switch from normal hexokinase to hexokinase II not only allowed cancer cells to compensate for the energy lost due to loss of and damage to mitochondria, but it also immortalized the cancer cell, turning it into a voracious, gritty, enduring, version of a normal cell.
Pedersen’s lab then made another discovery in 2003. In addition to its hysterical consumption of glucose and its impediment of apoptosis, hexokinase II positioned itself perpendicular to a protein called ATP Synthasome, a rotating machine-like protein that belched out the cellular energy currency, ATP. Hexokinase II’s positioning allowed it to steal ATP before it had the chance to escape, putting the cancer cell’s insatiable appetite for glucose before other cellular needs. Like a plundering pirate, hexokinase II steered its ship next to and then tethered itself to the side of a merchant ship rife with treasure, unabashedly stealing its booty.
Throughout the 1970s, 1980s, and 1990s, and into the new millennium, while the genetics of cancer took center stage, Pedersen continued to uncover the details of the Warburg effect. For a disease that was thought to be a tornado of genetic chaos, his image of cancer was one of organization and coordination. It wasn’t incomprehensible, it was precise and simple. A single molecular transition to a parasitic isozyme was largly responsible for two hallmark features of cancer: the Warburg effect and evasion of apoptosis. And unlike Her-2, it wasn’t in a fraction of a single cancer type (one of two hundred different types, each one its own distinct disease). It was in all of them, just as the PET scans showed.
The potential of hexokinase II as a therapeutic target was not lost on Pedersen. And as the millennium approached, he decided it was time to zero in on it. He shifted the focus of his lab from basic cancer research to developing therapies using what they had learned, from basic science to applied science. But as seductive as the target was, it was surrounded by a moat. Even if Her-2/neu was a fleeting and impotent target, the important quality that it possessed, from a drug-design perspective, was accessibility. It hung in plain sight on the outer surface of the cell.
Pedersen faced a far greater challenge in attacking hexokinase II directly, because it sat comfortably protected inside the cell. To try to get to it, rather than target it directly, he attempted a backdoor approach, targeting hexokinase II from the level of gene expression. If he could prevent the gene from being transcribed into its protein product, he reasoned, maybe he could prevent its gross overexpression. This would turn off the Warburg effect and reestablish a path for the damaged cell to kill itself through apoptosis.
To do this, he employed a technique called antisense RNA. Theoretically, a single strand of RNA, complementary to the single-strand of hexokinase II messenger RNA, would bind—similar to Varmus and Bishop’s molecular “fishing pole”—and physically obstruct its translation into protein. It was a technique designed to “shoot the messenger” and prevent the final protein from being manufactured. But, like many others, Pedersen discovered that the technique was difficult to implement. As one commentator put it, “Antisense RNA is a technique gorgeous in concept but exasperating in use.”
As Pedersen floundered trying to get the technique to work, a new postdoc came to work in his lab in 1991. The lively South Korean, Young Hee Ko, would completely change his life.
Ko entered his lab with glowing recommendations. Four of her former professors wrote Pedersen on her behalf, and her doctoral thesis advisor, Bruce McFadden, wrote that one of her research proposals was “the best and most original…[he] could remember in twenty five years at Washington State. [Dr. Ko] is the most original doctoral student that he had in 25 years.” He went on to say, “Personally, Dr. Ko is delightful. She is very modest and self-effacing yet she is developing good critical powers. She is a very considerate lab colleague.” A member of Ko’s thesis committee, Ralph G. Yount (a president of the American Society of Experimental Biologists), wrote, “She is personally somewhat self-effacing but intellectually aggressive. I feel she would fit into almost any lab with little trouble. She has my highest recommendation. I wish she had worked for me!” Ko’s postdoctoral application came with “the highest recommendations I had ever seen,” Pedersen said.
Pedersen feared that the competitive environment of Johns Hopkins might prove difficult for Ko. “My first impression from her petite stature was that other students may try to take advantage of her. However, I soon learned that she had no problem in defending her turf.” Once she settled in with a project, Pedersen realized that Ko’s extraordinary recommendations were perhaps understated. Her small stature veiled an unrelenting focus, vigor, and capacity to work long hours. “She has never taken a vacation; she works seven days a week. She comes in at six or seven o’clock in the morning…and goes home sometimes after midnight. If you want verification of that, you can just ask the guards,” Pedersen told a reporter from The Baltimore Sun. “She moves passionately forward with her projects. She moves at lightning speed and works relentlessly day and night until she completes her objectives.” The man who overcame any deficiencies, perceived or otherwise, through gritty work ethic alone found himself awestruck by his new postdoc’s “superhuman” work ethic.
A South Korean by birth, Ko received an undergraduate degree from Kon- Kuk University in Seoul in 1981. The next year, she immigrated to the United States and enrolled in the nutritional physiology Master’s program at Iowa State University, where she graduated in 1985. Yet even with a Masters degree, Ko felt unsatisfied. She had grown to feel that nutrition only skimmed the surface and craved a “deeper understanding of the way life operated” at the most fundamental level, so she enrolled in the PhD program of biochemistry at Washington State University and completed it in 1990.
When Ko entered Pedersen’s lab as a postdoc, the laboratory was in the midst of several projects, one of which was researching the specific pathology of cystic fibrosis. Other labs had isolated the singular cause of cystic fibrosis: a mutated form of a protein known as cystic fibrosis transmembrane conductance regulator (CFTR). Inherited mutations in both copies of the gene left a cell unable to regulate the transport of chloride and sodium ions across membranes, a fundamental process. Victims of the inherited disease experienced a mosaic of symptoms such as lung infections, gastrointestinal problems, and endocrine issues.
Ko was assigned the task of finding out why the mutated protein was dysfunctional, a task particularly well suited to the skills she acquired while earning her PhD. True to her nature, she dove into the project with reckless abandon. Seven years and seven publications later, she and Pedersen felt that they had found the reason behind cystic fibrosis’s faulty protein. “It was a localized folding problem resulting in dysfunctional CFTR,” Ko said, summing up the years of research in a single sentence. The victims of cystic fibrosis had a faulty codon that resulted in a missing amino acid or the wrong amino acid within the CFTR protein, thus changing its three-dimensional architecture and rendering it dysfunctional.
As the new millennium approached and the work on cystic fibrosis completed, Pedersen directed Ko to his lab’s marquee endeavor: cancer. To treat cancer, they knew what they had to do. They had to attack hexokinase II, the protein they felt was the beating heart of cancer. Pedersen set Ko on a task with a single focus: by whatever means possible, isolate and inhibit hexokinase II. By now it was clear to him that Ko was special. They had been working together for a long time, and Pedersen had developed a new appreciation of her, describing her as “simply the best scientist that has ever worked in my laboratory in its thirty-four-year history.” As such, he knew he was better off stepping aside—for the creative process to work, it was best to surround a goal with an empty matrix so that the imagination could approach the center unencumbered. As he expected, she attacked her goal with the vigor she was known for.
Ko recognized the futility of targeting hexokinase II with the antisense RNA method. “I suspected the antisense RNA wouldn’t work,” she said. Rather than emulate Pedersen’s backdoor approach, she set out to find something that might inhibit hexokinase II directly. Like Pedersen, she faced the vexing problem of getting something into the cancer cell. She began working the problem backward, looking at the target before deciding on the bullet. By virtue of Pedersen’s continuum of work, Ko knew, as Warburg proved more than seventy years earlier, that cancer cells overproduced lactic acid. She knew that the cell had to get rid of the corrosive waste product immediately, or it would kill the cell from the inside out, like carbon monoxide poisoning from an idling car in a shut garage. Being the survivalists they were, cancer cells overproduced a membrane-imbedded protein called a monocar-boxylate transporter (MCT). The porous protein acted as a door, selectively allowing lactic acid and pyruvate (pyruvate is similar to lactic acid) to enter and leave the cell.
Ko realized that cancer cells produced many more of the “doors” than normal cells. Essentially, the door for a molecule that “looked like” lactic acid or pyruvate, typically shut on normal cells, was left wide open on cancer cells. The difference was the disparity she needed and the opening she would exploit. During quiet moments, when she thought about how to take advantage of the opening, she circled back to a molecule that she had worked with while a PhD student at Washington State University called 3-bromopyruvate (3BP). It was a three-carbon molecule that shared the same chemical structure as pyruvate except for a single difference: one atom of bromine replaced a hydrogen atom. She thought it was close enough that the MCT protein wouldn’t be able to tell the difference. It differed by a single atom and might be able to slip through the door unnoticed like a molecular Trojan horse. In addition, the atom that distinguished 3BP from normal pyruvate might add the reactive punch needed to mortally damage hexokinase II once inside.
Ko knew it was a long shot, but it was worth a try. The idea was elegant in its simplicity, but it seemed far too simple. Could cancer really have left a door wide open? Could an effective therapy come from a molecule so simple, so common, and so well known that it could be ordered from the shelf at any chemical supply house? Cancer was infinitely complex—Ko had read the textbooks. It was caused by a web of pathways so tangled and intertwined that it was going to take decades, if not millennia, to sort it out. There was no way this overly simplistic line of reasoning could work, but every time she walked through the logic, she failed to find a reason why it wouldn’t work. So unknown to everyone in the lab, even Pedersen, she ordered a batch of 3BP from a chemical supply house.
Once the package arrived, she decided to compare 3BP with a dozen other metabolites that may or may not have anticancer properties. She added the chemicals directly to cancer cells growing in a petri dish, comparing the compounds head to head. 3BP immediately jumped out as the best candidate. “Initially I was surprised by how well it worked compared to the other compounds I was screening alongside it,” Ko said. Testing its cancer-fighting prowess compared to a small list of unknown compounds was one thing; but it would also have to prove that it matched up against the chemotherapeutic heavy hitters. “I ran the first assay where I compared 3BP against carboplatin, cyclophosphamide, doxorubicin, 5-fluorouracil, methotrexate, and paclitaxel, and I thought something was wrong. 3BP was killing the cells so much faster,” Ko said. “I just couldn’t believe it, so I ran the assays, I’m not kidding, over one hundred times.”
Every time she ran the assay, she saw the same stunning result—3BP wasn’t just better at killing cancer cells than conventional chemotherapy drugs, it was vastly better. Even more shocking, it was vastly better in every type tested: brain, colon, pancreatic, liver, lung, skin, kidney, ovarian, prostate, and breast cancer. In every sample, 3BP dominated the list. As any cancer researcher knew, it was best not to get excited too quickly. Testing drugs in a petri dish was one thing, but testing them in the complex and nuanced environment of a living organism was a different game. Many drugs that appeared great in a petri dish either failed to work in animals or displayed an intolerable cadre of side effects.
Having exhausted the limited experiments she could perform in petri dishes, Ko knew it was time to tell Pedersen about 3BP and request to try it in animals. “It will never work,” he said, when she approached him about testing 3BP in rabbits. “It’s too reactive.” He knew the inherent chemistry of molecules with similar structure imbued them with hyperreactivity, an itchy trigger finger. As he weighed the idea of testing 3BP in animals, his initial thought was that it might be a fool’s errand at best and maybe immoral at worst. He thought that the jittery molecule would instantly and violently react before it had the chance to slip inside the cancer cell, most likely killing the animal in the process.
Ko talked to her mentor at Washington State University, and he told her the same thing. “You could waste your whole career trying to figure out how to make it less reactive,” he said.
Her persistence eventually wore Pedersen down, and he agreed. They decided to try 3BP in a rabbit model of liver cancer (rabbits surgically transplanted with skin cancer from a common donor into their livers). Still convinced that it was a waste of time, he watched from the sidelines. “I felt sorry for the rabbits,” he said. The rabbits were injected one by one. If 3BP was going to kill the rabbit, it would probably happen soon after injection. As the tense moments passed and the rabbits continued to hop around, seemingly unfazed, they realized that 3BP might not be as toxic as Pedersen had thought.
The next morning, having barely slept, Ko went to check on the rabbits. She found them in what appeared to be perfect health. They were eating, milling around, and acting as if nothing had happened.
After several uneventful days, it was time to test the results. The rabbits were sacrificed, and an autopsy was performed to see if 3BP had had any effect on the tumors. The reactive drug had not produced any of the obvious side effects that Pedersen and others had predicted. The more substantial hurdle, determining if the drug had any meaningful impact on the tumors, remained to be overcome.
They surgically removed the tumors from the control rabbits that did not receive 3BP. As expected, the slides under the microscope displayed 100 percent active, dividing, cancer cells. The next slides contained samples from the rabbits given 3BP, and what they saw was “quite dramatic,” they wrote. Every sample contained almost all dead, necrotic cells. They looked at the normal liver tissue surrounding the tumors, suspecting that the battle lines may not have been perfectly drawn and the toxicity that killed the cancer cells may have bled over into the normal tissue. The margins were clean—even the surrounding liver tissue was healthy. Everywhere they looked, it appeared that the twitchy molecule spared normal tissue—lung, kidney, brain, heart, stomach, colon, muscle, and small intestine. Every tissue examined appeared unaffected. “That’s when I realized we were on to something big,” Pedersen said.
As exciting as the petri dish and rabbit experiments were, the next experiment proved even more so. Pedersen and Ko decided to go from the start all the way to the finish line. They would attempt to cure rats of aggressive, advanced liver cancers, thereby restoring their normal life span. Rather than a single 3BP injection, they gave multiple injections over the course of weeks, a true test to see what the drug was capable of. The trial contained two groups: one that received 3BP and a control group that did not. As expected, the control rats quickly succumbed to the aggressive cancer, living only weeks. As the last of the fourteen control rats died, the 3BP group—all nineteen rats, even the ones with the most aggressive metastatic disease—continued to live, transcending the invisible-barrier of inevitability defined by the disease.
As the weeks passed and the animals continued their regular treatments, one PET scan after the other, incomplete by themselves, began to form a picture: the rats were being cured, completely cured. The weeks turned into months, and the rats appeared healthier than ever. “They were enjoying life again,” Pedersen said. Every rat treated with 3BP lived a normal lifespan, and the cancer never returned. “I’ve been in cancer research for twenty years, and I’ve never seen anything like this that just melts (tumors) away,” a veteran cancer researcher said.
Every potential cancer drug had to go through a series of steps to get to the ultimate destination: treating humans. The road was littered with the corpses of drugs that failed the journey. Throughout the 1990s, only 5 percent of oncological drugs that entered clinical development received approval. Worse, 60 percent of the drugs that failed did so in the middle of phase three studies, after millions of dollars had been spent. Human trials were the only way forward, because they alone determined whether a drug provided any benefit.
The Good, the Bad, and the Ugly
For 3BP, the transition to a human trial was anything but smooth. Balanced on the edge with the potential to change the course for so many desperate cancer patients, 3BP became embroiled in bitter scandal. The exalted qualities of human nature, curiosity, compassion, and logic that gave birth to 3BP had their lesser relatives derail its upbringing. As Ko put it, “This is when the bad stuff started to happen.” Pedersen called the discovery of 3BP and the events that followed “the good, the bad, and the ugly.” According to a Complaint filed in the United States District Court for the District of Maryland, Ko’s problems began in 2002 when she was offered a three year contract to serve as an assistant professor in Johns Hopkins’ Radiology Department. According to Ko, the job came embedded with an insurmountable problem. She was not given her own independent lab space, which, as a research scientist, put her in an awkward situation. The problem was summarized in the Complaint: “It is very difficult to obtain grant money to conduct medical research (approximately one in ten to fifteen grants applied for is awarded)….It is virtually always required to have one’s own laboratory space in which to conduct a project or study in order to demonstrate the principle investigators independence.” Ko found herself in a strange catch-22. She could apply for grants, but because she wasn’t given her own lab space, she was virtually assured not to be awarded the grant money. The smoldering problems fully ignited in the summer of 2003, shortly after the 3BP/rat study, when Ko applied for a prestigious Susan B. Komen grant to study the effects of 3BP on breast cancer. When she received word that she had been awarded the grant Ko was ecstatic. “It was one of the happiest days of my life,” said Ko. She had two reasons to be happy. First, the high profile grant would allow further investigation into 3BP’s cancer fighting potential, moving the compound one step closer to clinical trials. Second, with the grant, Ko was under the impression she would finally receive her much needed laboratory space. According to the Complaint, Ko had a letter from the former Chair of the Radiology Department, Dr. Robert Gayler, promising Ko laboratory and office space if she was awarded the Komen grant and if approved by [the standing Vice Dean for Research] Dr. Chi Dang. “But my happiness only lasted one hour,” said Ko. Elated by her new grant Ko approached the new Vice Dean of Research about her promised laboratory space. After meeting with Dang, Ko heard her email box ping. It was an email from the Vice Dean Dang with five others copied in, stating that Ko’s grant submission was “in fact, misleading to the Komen foundation.” Stunned, Ko approached the Vice Dean to find the basis of the accusation. The confusion was isolated to a single detail. According to the Complaint Dang assumed that the grant submitted to the Komen Foundation, like the vast majority of grant applications, required that an applicant already have laboratory space— the insurmountable catch-22 Ko was captured. “But the Komen grant application had no such requirement, they didn’t even ask the question about lab space,” said Ko. For Ko, the accusation carried more of a sting for other reasons. Years earlier, a research meeting had been convened in which faculty members were asked to discuss what they were working on. When it was Pedersen’s turn he talked about his lab’s exciting work with 3BP. Pedersen explained he and Ko remained cautiously optimistic 3BP might turn out to be a legitimate anti-cancer drug. According to the Complaint, the laboratory headed by Dang then “immediately requested some 3BP for use in the laboratory.” As time passed, Dang’s laboratory even requested Ko and Pedersen’s expertise. The Complaint states that Ko spent 80 hours on one assay alone, both conducting and writing up the research for the other laboratory. On another occasion a member of Dang’s laboratory visited Pedersen’s lab to seek assistance from Ko regarding hexokinase II research. To Ko and Pedersen’s surprise, Dang’s lab was steering their efforts toward research Pedersen’s lab was already focused on. Nevertheless, according to the Complaint Ko spent over 30 hours teaching a student how to assay hexokinase, saving Dang’s lab an estimated 2 to 12 months’ time. Ko was shocked that with all her donated time helping others, and the fact the Komen grant application did not request information regarding the applicant’s access to laboratory space, she was not being congratulated and given the laboratory space that she felt had been promised to her. Ko clearly felt she was being subjugated to a double standard. Dismayed, she demanded the Vice Dean apologize for the email stating that her application had misled the Komen Foundation. To Ko it felt like her career and research were deliberately being sabotaged. But the situation had escalated too far—both sides had become so galvanized that a compromise couldn’t be reached. On April 22 Ko was handed a letter stating that her continued faculty appointment was contingent upon her receiving a psychiatric evaluation. “I was pissed off,” said Pedersen. “Here is this person trying to cure cancer and she is being treated like this.” In a moment of more thoughtful reflection Pedersen isolated the problem to one of misincentives. “It is wrong to put people doing research in charge of others doing research—scientists at this level are competitive, you’re just asking for trouble. Others with control of lab space were doing research which overlapped with ours, it’s the perfect set-up for a bad outcome.” Pedersen had been at Hopkins long enough to know the disciplinary process Ko was being subjected to was far from perfect. “The psychiatric evaluator is likely to work with the accuser,” said Pedersen. “I knew this was not going to have a good outcome. It was the first step out the door.” Ko refused the evaluation because “she did not wish to be perceived as a scientist accused of having an unsound mind and any treatment of this kind could become part of her permanent record.” Knowing full well refusal of the evaluation would likely result in her termination, on June 1, 2005 she filed a 108 page complaint in the United States District Court for the District of Maryland alleging discrimination, retaliation and a number of state torts claims. In the winter of 2005, just as tempers were beginning to calm, a reporter for The Baltimore Sun ran an award-winning three page article about 3BP entitled: “Young researcher stalks cancer: With little life outside the lab, a Hopkins worker studies a chemical that shuts down tumors in rats.” According to Ko, the top-brass at Hopkins thought it was irresponsible and premature to be touting the promise of 3BP, and in an instant the entire situation was once again ignited, starting a renewed round of friction, again hampering Ko and Pedersen’s work. The lawsuit was finally settled in 2006. The conclusion of the lawsuit upheld two patents. The first was a patent shared between Pedersen, Ko, and an M.D. named Jean-Francois Geschwind. In the winter of 1999 Geschwind had entered Pedersen’s lab as a research science student. Laboratory experience looks good on a resume, and students often ask professors if they can help in the lab to gain bench experience. Pedersen didn’t know it at the time, but looking back he said letting Geschwind into his lab was “the biggest mistake of my career.” Geschwind was put on the cancer therapy project, and eventually on the 3BP/rabbit study. According to Ko’s Complaint his overall contribution was to guide the catheter into the hepatic artery and “push the plunger.” But “naively,” said Ko, Pedersen included Geschwind’s name on one of the publications relating to 3BP. Pedersen also included Geschwind on the first patent application regarding 3BP’s anticancer capacity, “Not realizing that there are differences between inventorship and authorship,” said Ko. So even though allegedly he had little to do with the discovery and development of 3BP, Geschwind was included on the first patent application filed. The patent, shared with Johns Hopkins University, was for the intra-arterial delivery of 3BP to treat hepatic cancer in the United States. The second patent application filed in 2006 gave Ko exclusive rights to her proprietary formulation of 3BP to treat 100% of all PET positive cancer types both within the United States and abroad. And according to Ko, the formulation is everything. The formulation alone allows 3BP to achieve the necessary concentration to treat cancer. Also, the formulation prevents 3BP from reacting too early, mitigating toxicity. With the lawsuit settled, Geschwind quickly took advantage of the first patent bearing his name. He went on to found a company called PreScience Labs. The company’s stated mission: “To develop powerful, effective and safe anti-cancer agents by disrupting tumor metabolism.” In 2013 the company received FDA approval for the immediate enrollment of a phase 1 study using 3BP to treat metastatic liver cancer patients. According to the company’s website, and a 2013 telephone conversation with the company’s president, Jason Rifkin, they are still trying to procure funding for the phase 1 trial. In the end, the damage had been done. 3BP’s delicate march toward human trials had been sidelined in a multi-year lawsuit. Ko left Johns Hopkins, leaving Pedersen’s laboratory with an undeniable void—a hole in the center. The once vibrant, bustling, laboratory was without its star researcher. But the real tragedy existed beyond the hushed conversations and busy lawyers; beyond the hurt feelings, anger, sanctimony, and bitterness. The real tragedy was an ephemeral abstraction—it was the untold damage that remained hidden from view. The real tragedy was best represented by Ko’s empty flasks, pipettes, and other equipment that now sat idle, and began to collect dust—the real possibility that lives might have been saved by 3BP. How many? No one will ever know. Without her work space—the environment that had been her entire life for over a decade—Ko retreated, isolated herself, and focused on her work with a singular purpose – developing an almost maternal attachment to 3BP and its potential to help people. “I haven’t done anything else with my life,” admits Ko, “so this is my baby.” In the summer of 2008 she felt the formula was finally ready to enter a human trial. Typically, a drug will first establish if it has any efficacy by performing a “case study” on a single individual before going on to larger trials. Ko wouldn’t have to go looking for a case study; in fall of 2008 one came to her. She received an e-mail from the father of a dying son, pleading for her help. The father’s name was Harrie Verhoeven, and his son was Yvar. They lived in the small town of Schjindel, in the Netherlands. After exhausting every option to treat his son’s cancer, a desperate search had led him to Ko. It was his son’s last chance. “It was so moving,” she said. “I think 3BP really was the last chance for his son.” “If I Hadn’t Seen It with My Own Eyes, I Wouldn’t Have Believed It” Almost a decade after Ko stared in amazement as 3BP made a who’s who list of FDA-approved chemotherapy drugs look like amateurs (and then went through the crucible of drama), the drug with so much potential got the chance to help somebody. A human trial was necessary for the maturation of the adolescent drug. It would work, it wouldn’t work, or it would prove too toxic. In any case, it would be a big step in determining the drug’s future. The story began a year earlier when, out of nowhere, Yvar noticed that he was burping a lot, an annoyance more puzzling than concerning for the teenage boy. A month passed and another, and the burping continued. “Stop burping, Yvar!” his mother scolded him, thinking that it was nothing more than the insolence of a sixteen-year-old. In another few months, what had begun as an inconvenience had progressed into a terrible annoyance; he was burping constantly. His family began to think that something might be wrong. Though it appeared to be nothing more than a mild digestive issue, they made an appointment. The doctor agreed with the family. It presented like a mild case of intestinal gas, it could be any number of things—a stomach bug, too much spicy food, or too much soda, but it was nothing to be concerned about. He prescribed stomach acid suppressors and sent them on their way. He noted that when he palpated Yvar’s stomach, the boy had some mild enlargement of the liver, but the doctor told them not to worry. Along with the intestinal gas, it would most likely pass. Yvar settled into his normal routine, hanging out with friends and practicing taekwondo. He was one of the youngest students in the Netherlands ever to receive a black belt, and trophies and ribbons from European tournaments were scattered throughout his room. But rather than subsiding, the burping only got worse. He burped continuously, even in the middle of sentences. The medication had not worked. August 9, 2008, began like any other day. It was a typical summer morning, and Yvar was playing Xbox online with his American friends. “I could hear him yelling and cursing at the game from the other room,” his father said. “Then I heard Yvar scream in pain, so I ran into the room, and he was clutching his abdomen. He was pale and cold and covered in sweat.” His family helped him to the car and rushed to the emergency room. “He was in terrible pain,” his father said. At the emergency room, the attending doctor palpated his stomach. Yvar’s liver was enlarged, as was his spleen, and his temperature was high. The doctor ordered blood work for liver enzymes, a measure of liver distress. When the results came back, Verhoeven noticed the doctor seemed panicky. The team shuttled Yvar and his family into a separate room, where the doctor explained that the boy’s enzymes were fifteen times what they should be. One possible explanation was cancer, but liver cancer at the age of sixteen was almost unheard of. Whatever the culprit was, it had transcended some fragile biological barrier with frightening speed, no gradual prelude of symptoms. Something had snapped, presenting with alarming suddenness. Scans were scheduled for the next day. In the morning, Yvar underwent a CT scan, an MRI, and a PET scan, and all came back with the same terrible image. He had hepatocellular carcinoma. His liver was consumed by it—fist-sized masses had taken over 95 percent of the organ. The images showed that it had spread with uncommon vigor, even landing on his heart. The sudden turn of events, and the horrible quickness they unfolded in, left him and his family in shock. What a few days ago was an innocent case of unexplained intestinal gas had, in a few hazy moments, turned into the delivery of a death sentence. The tumor was far past operable, so transplant was the protocol for such a dire case. But even that was not an option, the doctors explained, because Yvar’s tumor had spread so aggressively he was not considered a candidate. There was some sober talk of trying chemotherapy but less for the outcome and more because they had to try something. He was too young to be sent home to die. Even so, the doctors told him and his family the brutal truth. Yvar probably had less than three months. He probably wouldn’t live to see his seventeenth birthday. A week after the diagnosis, Yvar received a call from his doctor. Finally it was good news. Nexavar, a chemotherapeutic drug approved for kidney cancer, had received orphan drug status for liver cancer. It was a stroke of good fortune in what was a hopeless situation. Finally they could feel a scrap of hope. Even though it was largely untested and Yvar would be the youngest patient ever to receive the drug, it was something. Nexavar was one of a new generation of “targeted drugs” designed to target a cancer cell’s malevolent machinery with exquisite precision. It specifically targeted tyrosine kinases, a group of proteins often implicated in the pathogenesis of cancer. But tyrosine kinases also serve healthy cells, and a drug’s ability to distinguish between the two overlapping proteins determined how well the drug worked and the magnitude of side effects. Initially the drug worked. Yvar’s tumors at least halted their unrelenting expansionary march. But the initial response, as is so often the case, proved to be short- lived. The drug was a single move in a chess game, and the cancer had already countered it and moved ahead. With Nexavar no longer effective, Yvar was again hopeless. His health was in free fall. The methodical subversion of what was left of his liver was releasing a steady stream of toxic shrapnel into his bloodstream, sending him in and out of consciousness. His father quit his job at a university-related institute where he worked as a plant molecular biologist to take care of Yvar full time. He searched the Internet at night, hoping to find anything that might help. He had a head start. Because of his education and training, he knew where to look. His search lead him to Evangelos Michelakis at the University of Alberta, the man responsible for the discovery of dichloroacetate (DCA), the molecule that had received a brief spike of attention for the preclinical promise it exhibited on a variety of cancers. “But Yvar didn’t qualify for DCA, I was told,” Verhoeven said. With little time, he shifted his focus to a molecule called 3-bromopyruvate. He had heard about the preclinical work, and The Baltimore Sun ran a punchy article highlighting the promise of the experimental drug, explaining how the molecule rid nineteen rats of advanced liver cancer. The drug operated in a different way than traditional cancer drugs, attacking the defective metabolism of the cancer cell. Further research into the drug exposed the fact it was highly reactive and could prove dangerous if not administered correctly. It was a simple, cheap molecule readily available at most chemical supply houses and wouldn’t be hard to get. He thought about ordering it himself, but he knew that the formulation was key, and the reactivity of the molecule might push Yvar over the abyss. His son’s life was balanced on a knife’s edge, delicately sustained by the sliver of healthy liver tissue he had left. Verhoeven contacted Young Ko of Johns Hopkins, the woman responsible for the discovery of 3BP’s anticancer ability, knowing that she knew every nuance of 3BP, the right dosage, and the proper formulation. If Yvar was to get 3BP, Ko would have to help. Time was critical, because Yvar was in awful shape, and his father knew that each day could easily be his last. As he explained the situation to Ko, she was moved to tears. She couldn’t help but feel deep compassion for the desperate father and his dying son. She had come as close as she could to perfecting the formulation, crucial to keep the twitchy drug from reacting too early once in the body. She felt that 3BP was ready. She dropped everything, channeling all her time and prodigious energy toward helping Verhoeven and his son. She needed to find a doctor willing to administer the unknown drug, and this proved harder than expected. The search devoured the one thing Yvar didn’t have: time. Together with her assistants she decided on a shotgun approach and sent more than five hundred e-mails to doctors throughout the United States, explaining the situation and hoping that one of them would have the courage to administer the drug. It was a long shot. One of the hardest parts of getting a new drug through trials was finding doctors willing to take the inherent risk. When she didn’t hear back from any of the requests, she turned to a friend who knew a doctor in Germany who might be willing to help. European doctors had more discretion than American doctors, and they were more inclined to try experimental drugs and procedures in patients with no other options. Ko contacted the doctor, Thomas Vogl, at the University of Frankfurt. Vogl was a world-renowned expert in a pioneering process of drug delivery called transcatheter arterial chemoembolization (TACE), which involved snaking a tube from artery to artery until it reached the vessel directly feeding the tumor. It moved the chemotherapeutic battle line from one of random diffusion throughout the body to a direct and forceful assault. More than five hundred doctors shied away from helping with the unknown drug, but Vogl stepped up, knowing that it was Yvar’s last chance. But first permission to administer the experimental drug would have to pass the University of Frankfurt’s ethics board, a process that would eat away another precious month. As the weeks passed and the ethics board continued its deliberative process, Yvar’s condition was dire. “The doctors had no idea how he was still alive,” Verhoeven said. Vogl decided that he had to try to buy Yvar some time—he would use TACE to try to at least pause the tumor’s relentless subversion. Vogl guided a catheter on an interarterial journey beginning in Yvar’s groin and landing in the vessel supplying the tumors. Vogl then delivered gemcitabine and cisplatin, two highly toxic drugs shown to evoke a slight response in liver cancer but unable to increase overall survival. “It was a desperate attempt to just get Yvar to where we could get him the 3BP, he was so sick,” Verhoeven said. The cytotoxic drugs may have beaten back the tumor and bought Yvar some time, but the drugs racked him with unremitting fits of nausea, further compounding his misery. Knowing that approval was pending, Ko traveled to Germany to help administer 3BP. When she arrived, she was shocked by what she saw. “When I got there, Yvar was in horrific shape. He was skin and bones, and his arms were yellow and bruised. He couldn’t eat, and he had a feeding tube. He had to sleep sitting up because the tumors were so large they stretched his abdomen when he tried to lay back, and he was throwing up so much he didn’t just have a bucket next to him, he had a barrel,” Ko said. In Vogl’s office, they discussed the trial, dosage, timing, and delivery. Ko couldn’t help but notice the commotion going on—men were scurrying around with what appeared to be camera equipment. She learned that a documentary was being filmed on the actress, Farrah Fawcett, and her struggle with cancer. Fawcett’s battle had led her to Vogl and his TACE technique. Her cancer had spread wildly, and all attempts to combat it had proved ineffectual. Moved by her story and stoic courage, Ko urged Vogl to help her and to give her 3BP. It was too late; her cancer had spread too far and they didn’t have the time to jump through the hurdles. On February 29, 2009, a year and a month after Yvar’s original diagnosis, the ethics committee agreed to allow him to be treated with the experimental drug. Vogl and Ko decided the best route of delivery was via TACE. Due to 3BP’s reactivity, the closer it could be delivered to the tumor, the better. Ko’s patented preparation would also be key. It was a process she likened to “adding layers, like an onion, that were peeled off one by one, delivering waves of the active drug to the cancer cells.” Yvar’s situation was so dire that the duo decided to inject him twice the first day for a total dose of 250 ml. “I considered checking Dr. Ko into the emergency room while we were injecting Yvar with her drug. She was so utterly consumed with nervous excitement we thought she might faint,” said an assisting nurse. “In the end, she composed herself enough to remain present.” There was nothing to do but wait. Ko said, “I was so nervous to finally see 3BP enter a person, and you just don’t know if there are going to be side effects.” Yvar received the injection at two o’clock. By three o’clock, he was still feeling okay with no immediate side effects, unlike the other cytotoxic chemotherapies that had hit like a ton of bricks, bringing on waves of nausea. At four o’clock, there was no nausea, temperature, or rash. At five o’clock, Yvar stirred, smacked his lips, and said, “I feel hungry.” He hadn’t been able to eat for months. “When he said he was hungry, we all began to cry,” Ko said. “It was such an emotional moment. Maybe the drug was working that fast.” A week later, Yvar received another injection of 3BP via TACE. Again, no immediate side effects were observed, and he was allowed to return home, but a mild case of light-headedness turned into confusion. “He didn’t know who we were and began acting very agitated and aggressive,” Verhoeven said. By the next morning, Yvar was in a coma. “I called the hospital, explaining the situation. Basically they told me that Yvar’s situation was hopeless, and I needed to just let him die.” Verhoeven suspected that he knew the problem. The ambulance brought Yvar to the emergency room, and again the desperate father found himself having to convince the attending physicians to treat his son. They balked, running through the diagnosis in their minds. With end-stage liver cancer, there was nothing left to do but palliative care. His desperation persuaded the doctors to order a battery of blood work, casting a wide diagnostic net to snag the culprit. They soon had their answer: ammonia. Verhoeven had suspected as much. Yvar’s sky-high ammonia levels were the result of tumor lysis syndrome, a rare syndrome caused when massive quantities of cancer cells die a sudden, disorderly death, releasing their toxic payload into the blood stream. Not only was 3BP working, it was working too well. The side effects of the tumor lysis syndrome proved to be transient, and Yvar woke up. The doctors watched him for a while and allowed him to go home by nightfall. “Everybody breathed a huge sigh of relief,” Ko said. When the time came for the next treatment two weeks later, they were prepared. Yvar was given Hepa-Merz, a drug that removed excess ammonia and negated the toxic effects of tumor lysis syndrome. His ammonia levels began to rise, showing dramatic evidence for the efficacy of the drug, but he remained conscious and experienced only mild nausea. The next five treatments, each given about two weeks apart, went smoothly. By the summer, four months after starting treatment with 3BP, he began to regain strength. His 24-hour feeding tube was removed, and he was enjoying the foods he liked. He regularly left his wheelchair for walks. He was hanging out with his friends, playing Xbox, and cursing at the TV as he lost himself in the moment. In September, six months after Yvar began treatment with 3BP, Ko flew to the Netherlands to celebrate his eighteenth birthday. “It was absolutely wonderful,” Ko said. “The doctors told him he wouldn’t make his seventeenth birthday, and here we were celebrating his eighteenth, and he was getting stronger every day.” After his ninth treatment with 3BP, Yvar went in for CT scans. The scans were compared to the images at the time of diagnosis to determine how effective the 3BP treatment had been, and the difference was stunning. The “before” images depicted a liver full of active malignancy, with the surrounding lymph nodes and spleen subverted by the disease. The “after” scans showed necrotic, encapsulated tumors surrounded by normal lymph nodes and a normal spleen. The fluid surrounding the liver, once full of free-floating malignant cells, contained none, suggesting complete eradication. There were no signs of active cancer cells, only a scorched battlefield. Even the battlefield was beginning to clear; Vogl detected evidence of liver regeneration—life emerging out of the ashes. “This is something we have never seen before,” Vogl said of Yvar’s regenerating liver. Every test led to the same inescapable conclusion: 3BP had eradicated Yvar’s cancer. Two months later, Yvar accepted an invitation from Pedersen and Ko to come to Johns Hopkins and speak about his experience with 3BP in front of the university’s first-year medical students. He was feeling better every day, so his family planned a vacation around the event. After the talk, they would fly to Utah, rent an RV, and tour the Western United States. “We are planning on going to the Grand Canyon, which my mom wants to see. I want to go to Vegas,” Yvar said to the laughing medical students as they chatted after the presentation. After the RV tour, they planned to return to Salt Lake City, where they would spend Thanksgiving with family. They would fly to New York City for another round of sightseeing before returning to the Netherlands. The students graciously thanked Yvar and his family for coming. It was a something far outside the normal routine. “Thank you too, I’ve already had so much fun,” Yvar said with a big smile. Shortly after they returned home, Yvar came down with pneumonia. No one can be sure where, or how, he acquired it. He had won his war against cancer, but the fight had been costly, unfortunately nobody knew just how costly it had been—not his father, not his doctors, not Dr. Ko. So much of his liver had been subverted by the disease that even with the cancer eradicated he was left with a tiny portion of functioning liver, roughly just five percent. And although his liver was in the process of regenerating, Yvar’s health was left hanging by a tenuous thread. As Ko recited Yvar’s story, she stopped numerous times, her eyes welling with tears, her voice trailing off as if imagined scenarios coursed through her mind. “If only we had kept him in a bubble until he was stronger and his liver was more mature.” The antibiotics he had no choice but to take required a healthy liver to process, and they were too much for the portion of liver he had left. Yvar did not die of cancer. A CT scan performed shortly after he contracted pneumonia told the story. There was not a living cancer cell found anywhere in his body. He was lost to the damage the cancer had done, but the distinction was meaningful. The experimental molecule that operated in an entirely different way from all other cancer drugs had done something miraculous. “If I hadn’t seen these results on my own equipment, with my own eyes,” Vogl said, “I would not have believed them.” In the summer of 2009, with Yvar’s trial nearing its completion and four years after The Baltimore Sun article, word about the blockbuster potential of 3BP found its way to the top. Pedersen and Ko felt that 3BP was more than ready to enter large-scale trials and once and for all prove its efficacy to the world. Ko shared a mutual friend with billionaire David Koch. Aware of her work with 3BP, the friend informally told Koch of the excitement surrounding the new drug. During the conversation Koch expressed an interest, wondering if the drug could possibly treat prostate cancer. The mutual friend then approached Ko, relaying that Koch might be interested in funding research for 3BP’s effect on prostate cancer. To move forward, Koch requested preliminary data to see if the experimental drug warranted his support. Excited by the possibility of funding, Ko got to work, quickly compiled evidence substantiating that at least within a petri dish, 3BP was active against prostate cancer. She learned that Koch used James Watson as his science advisor, so all the data would have to flow through him. “I handed the data over to Watson and then waited to hear back,” she said. The call soon came from Watson, inviting Pedersen and Ko to come to Manhattan and discuss the next step over lunch. On an unusually hot day in August, Pedersen and Ko made the three and a half hour trip to downtown Manhattan and met Watson at L’Absinthe, an expensive French restaurant on East Sixty-Seventh Street. Ko asked Watson if he had made the recommendation to Koch to fund her research. According to Ko, Watson admitted that he hadn’t said anything to Koch but had instead given the data to Lewis Cantley, Director of the Cancer Center at Weill Cornell Medical College and New York-Presbyterian Hospital (he cofounded the biotechnology company Agios, a start-up focused on the metabolism of cancer). To Ko it appeared as if Watson had handed the data to her competitor without her permission. She was astonished. “I gave him the data in confidence,” she said. “He wasn’t sorry or regretful.” “The lunch meeting quickly became tense,” Pedersen said. “I was just trying to keep things civil.” Ko said Watson then shifted direction and offered a new proposal. He was the chairman of the scientific committee for the Champalimaud Foundation, an extremely well-funded foundation dedicated to health related research. It was founded by the late Portuguese entrepreneur Antonia de Sommer Champalimaud. “Watson proposed that Pete and I hand over the data and let the foundation ‘take it from here.’ He wanted to take 3BP and just have Pete and I quietly go away,” Ko said. “Of course, I was reluctant.” With lunch coming to an end Watson surprised them by inviting Pedersen to come to Cold Spring Harbor in New York, the nonprofit research institute where Watson spent most of his career as the director and president, to give a seminar on 3BP. Pedersen accepted. When the day arrived to travel to Cold Spring Harbor, Pedersen asked Ko to accompany him to help field questions. “The presentation at Cold Spring was a disaster,” she said. “My computer stopped working. I’ve never had it stop like that. I couldn’t do anything for forty-five minutes. When we finally got it working, it was in read-only mode, so all the slides were in terrible resolution— you could barely read them.” In retrospect, she had a different take. “Maybe it was divine intervention, a message telling me not to reveal too much data.” “After the seminar, Watson kept hovering around her, trying to get her to reveal the formula,” Pedersen said. Suspicious of Watson’s intentions, she kept her information closely guarded. 3BP, the molecule with high and now widespread expectations, was still unfunded. After leaving Johns Hopkins, Ko is now at the University of Maryland BioPark. Her academic career has morphed into a fledgling biotech/pharmaceutical company called KoDiscovery LLC, exclusively focused on bringing 3BP to market. And the energetic BioPark was the perfect atmosphere for the transition. Pedersen and Ko certainly had to navigate choppy waters to get here. Some scars were obvious. Some remained hidden. One thing that survived the tumult was their working relationship. It was fatefully synergistic from the beginning. Pedersen, the last surviving member of Warburg’s fraternity, mapped out the target, allowing Ko to make the connection between 3BP and the altered metabolic landscape of the cancer cell. Pedersen was the wise old mentor, Ko his star pupil. They never questioned or doubted each other. They had each other’s back no matter what. But as remarkably productive as their union has been it has been equally tumultuous. The path for 3BP has been anything but smooth. Ko hasn’t exactly gone looking for trouble, but she has certainly bumped into her fair share. Without question the problems encountered at Hopkins have changed her, made her more guarded and suspicious of people’s intentions. “Young would do anything for the people she loves, she would walk to China for you if you asked her to,” said a close friend, “But I just wish she would look forward more than backward. She needs to move on from the past.” Most of their regret came from the fact that 3BP had been unnecessarily held up by the lawsuit. A drug with vast potential sat on the sidelines for almost a decade while tremendous numbers of people suffered and died. As was the case with all fledgling drugs, funding was the biggest hurdle, and today, it is more difficult than ever. Even Pedersen had difficulty getting funding for cancer research, and two of his recent NIH applications were literally thrown in the trash without a formal review. In January 2013, at his wit’s end, he sent a letter to President Obama, explaining the situation and urging him to fund clinical trials for 3BP. Not surprisingly, in the bureaucratic cobweb that exists, Pedersen received a standard “receipt” letter a year later from a staff member. The problems they had encountered after their discovery of 3BP now seemingly behind them, one has to believe that it is only a matter of time for 3BP to get the funding needed for trials. As the day I spent interviewing Ko and Pedersen turned to night, Ko kept jumping up, scurrying through the room, occasionally leaving to take care of some detail in her laboratory. Her mind was in continuous overdrive. Rumored to work eighteen hours a day, she didn’t answer when I asked her if it was true. She tilted her head to the side, neither admitting nor denying. When I received an e-mail at 2:36 a.m., it confirmed her epic work hours. “I have trouble sleeping,” she said. “I can’t turn off my brain.” It was clear that 3BP’s potential to save lives substituted for her sacrifice. When she spoke of the people she loved or helped, a warm smile took over her face. It was clear that she had developed a profound attachment to Yvar and his family and was deeply affected by his eventual death, saying, “if only we had kept him in a bubble, he would not have gotten pneumonia, and he would still be here.” As deeply compassionate as she was, it was clear that she refused to be pushed around or capitulate to injustice. She would dictate her destiny without giving an inch to anyone with questionable intentions. Her desire to control her surroundings was evident everywhere—every detail of the day was planned. As the catered dinner arrived, so did some friends, a short list of confidantes in her inner circle. The interview switched from the past to the future. Pedersen’s trusted accountant and his son (also an accountant but experienced in start-up companies and the process of raising venture capital) took over the conversation about the future of 3BP. Ko had made the transition from academic scientist to CEO of her own pharmaceutical company. She rattled off FDA requirements and the process for clinical trials. To move forward with a trial involving twenty or so patients, she estimated that she needed $3 million. She had an offer, “but it was a bad one,” because it grossly undervalued the potential of 3BP. But it seemed clear that it was not about the money for her. It was about recognition for her work and perhaps not wanting to give up too much control of 3BP, the drug to which she had devoted a large part of her life. One thing stood out as amazing. Because of the nature of 3BP’s target, cancer’s defective metabolism, Ko could pick almost any cancer she wanted for the initial trial. “If we choose kidney cancer, because it is rare, the FDA makes it much easier, costing less for applications and taking less time,” she said, “but we could also choose skin or brain.” Herceptin was able to target only 20 percent of a single type of cancer, allowing it to be prescribed for approximately fifty thousand cases of cancer out of 1.7 million overall diagnoses. GLEEVEC was prescribed for fewer than nine thousand cases each year or .5 percent of all diagnoses. In theory, 3BP could target any cancer that was “PET positive” (meaning that cancer was actively fermenting glucose via over-expressed Hexokinase II). Considering that this equated to about 95 percent of all cancers (the ones that were not PET positive were probably not growing, or growing slowly), the implication was almost inconceivable. If 3BP lived up to its promise, it could be the most important discovery in humanity’s battle with cancer since the dawn of time. In the large scheme of the cancer industry, 3BP needed an almost trivial amount of money to kick things off, so why wasn’t there more interest? Here was a drug that could revolutionize cancer treatments, yet where were the Ron Perelmans? Where were the patient advocacy groups that took over the front lawn at Genentech, absolutely demanding Herceptin?