The Compatibility Gene, page 15
It can still be debated exactly where people exited Africa from, if they exited only once, and where humans successfully spread to first, but it’s generally accepted that around 100,000 years ago humans successfully left Africa. About 50,000 years ago some reached Europe, and others entered the Americas at least 20,000 years ago. Important to the story of compatibility genes, relatively small groups of founders successfully populated each new territory. It’s been suggested, for example, that just hundreds or a few thousand modern humans made it across the Red Sea from East Africa to settle in Yemen and Saudi Arabia.35 Natural selection then acted on the founders’ gene pool as they adapted to the local environment – especially changes in climate, the available food and different types of infections.
Genetic analysis has even indicated that some of the variation in our compatibility genes probably came from us breeding with prehistoric, archaic, humans – Neanderthals and Denisovans.36 It is possible that the introduction of HLA variants into the modern human population through interbreeding was important in helping increase resistance to local infections. All this together – from human migration to interbreeding – underlies the current geographical structure of our genetic inheritance.
An outcome of this is that Africa retains the greatest genetic diversity in compatibility genes. Within the continent, there’s a close correlation between these genes and the different languages spoken – because human migration within Africa over the last 15,000 years has had a significant impact on both linguistics and genetics.37 Then across the world, diversity in our compatibility genes roughly correlates with distance away from Africa, becoming less variable in populations the further away from Africa – because migration to each new territory is seeded by a founding group of people.38
In some populations, HLA diversity is particularly limited; among the indigenous people of the Americas, for example, probably because they originated from particularly small founder groups. Brand new versions of HLA-B have relatively recently appeared in some. For example, distinct variants of HLA-B have been found in the Kaingang and Guarani tribes of southern Brazil, and the Waorani people of Ecuador.39 These versions of HLA-B are likely to be advantageous in fighting particular infections and their impact is perhaps especially important in a population that otherwise has relatively limited variation in HLA. Other rare compatibility genes are found in populations now living separately but related by a common ancestry, such as B*48, which occurs at relatively high frequency amongst Eskimos and other North American Indians, but rarely elsewhere.40
There’s also a geographical structure to the combinations of compatibility genes we each have. That is, many HLA genes occur together more often than would be expected from their individual frequencies. For example, the pairs of genes A*01 with B*08, and A*03 with B*07, both occur more frequently amongst Caucasians than would be expected by chance. A map of HLA types and their combinations in Europe marks out a boundary which corresponds to where the Alps are. Almost certainly this reflects how these mountains have been a barrier to gene flow during early stages of peopling the region.41
Overall, the current worldwide map of HLA types is an outcome of natural selection during our battles with infections and the pathways of human migration during the peopling of the world. The implication is that, broadly, our geographic heritage correlates with our susceptibility and resistance to various diseases – and even our response to some drugs.
Many places today are, of course, cosmopolitan, and a database used to keep information on people for potential transplant matches in the UK can reveal precisely how diverse we are.42 Amazingly, 268,000 people from across the UK are represented by 119,000 different combinations of compatibility genes. This is actually just an underestimation of the true level of our diversity, because the level of precision at which each gene was classified for this analysis was low. Even so, 84,000 combinations of compatibility genes were each represented by just one individual. Single compatibility genes can occur at relatively high frequency, but our complete set of genes is evidently personal: In this analysis, around one in three people were uniquely defined by their set of compatibility genes.
Although it remains to be seen exactly how important our individual compatibility genes may be in predicting the appropriate medicine for different diseases, it does seem unlikely that HIV, abacavir and HLA-B*57:01 will be a rare example. More cases like this are likely to emerge as we continue to probe the complexity of diseases. Compatibility genes may also correlate with our responses to vaccines, such as those commonly used for ’flu, polio, measles and rubella.43 This makes a lot of sense for our differences in class II genes, which encode the HLA proteins found on the specialized immune cells that play a role in initiating the kind of immune response key to successful vaccination. Population-specific vaccines may prove especially effective, though, in truth, we don’t yet understand what determines the length of time we remain immune after an infection or a vaccination.
Of course, compatibility genes are not the only genes that can influence our response to drugs. Rituximab, for example, a drug used to treat a certain type of cancer – lymphoma – works best for people with a particular version of another gene in our immune system.44 In fact, cancer is a prime candidate for treatments to be tailored to an individual’s genes. Myeloma, for example, is a cancer of immune cells in the bone marrow – and it is currently incurable. Life expectancies have increased over the last decade, thanks to new drugs, but not everyone responds to everything equally well. Across the world there are differences in treatments – the timing, combinations and doses of different drugs used in combination with stem-cell transplants all vary considerably. Much is decided on an ad hoc basis. Like many cancer treatments, personalized regimens are the norm – but the decisions are based on local expertise, far from being standardized.
The genetic make-up of myelomas from different people has been analysed and no single genetic factor causes this cancer.45 In fact, each myeloma cell has, on average, tens of genetic differences from the patient’s normal cells. Some mutations are common, including some involved in processes targeted by drugs already available. But a new opportunity has come from genetic analysis of myeloma; once again, instead of being defeated by the complexity, we could exploit it. Patients could have their cancer cells analysed genetically so that the appropriate treatment could be selected without wasting time testing drugs by trial and error – avoiding side-effects from drugs that can’t help. In this way, even though we don’t understand fully how the mutations combine to make a cell cancerous, we can just exploit the fact that it’s complicated to improve treatment.
It’s just an idea: it remains to be clinically proven. But there are many clinicians and scientists advocating that such personalized (or stratified) medicine should become a reality in the very near future. Technology for analysing genes currently improves about fourfold each year, and, if that continues, we’ll have sequenced the genomes of a million different people by 2016. That will be enough data to validate all kinds of specific genetic diagnostics. But there’s still a problem. One reason why this is not guaranteed to work out is that there can be great variety in the tumour cells themselves – even in a single patient. Even within one person, individual cancer cells can vary in their drug sensitivity. This situation is similar to what we saw with HIV: a highly variable enemy is more difficult to attack.
Viruses and tumours do something else that’s a problem – they actively thwart our defences. One way they do this is by trying to prevent our compatibility genes from working. It’s a battle; our immune system fights back by checking if compatibility genes have been interfered with. This involves a whole other function of our compatibility genes, a different way of looking at the immune system, and another set of immune genes that are also extremely diverse among us – in fact, they are probably only second to compatibility genes in how variable they are from person to person. This next piece of the canvas – hard-won by new heroes – reveals how compatibility genes can work in the exact opposite way to what we’ve discussed so far. Breathe it all in, embrace the complexity.
7
Missing Self
Klas Kärre would later chair the committee that decides the Nobel Prize in Physiology or Medicine, but in 1981, while writing his PhD thesis, he was less secure. Trying to summarize his observations in the last chapter of his thesis, he was puzzled by some data that didn’t seem consistent with the prevailing ideas about how the immune system worked. Kärre – described by his PhD supervisor, Rolf Kiessling, as soft-spoken, eloquent and slightly absent-minded1 – thought about the problem a lot. Others had come across the same discrepancies but just didn’t think them particularly important. What often distinguishes the great from the everyday scientists is their ability to think lucidly about observations that don’t fit with contemporary paradigms. As Leonard Cohen sings, ‘There is a crack in everything, that’s how the light gets in.’2
Once again, experiments in transplantation were at the heart of the matter. Recall that a transplant is rejected whenever it has proteins detected as non-self which cause an immune attack. But there was an exception to this rule – first observed in the 1950s by George Snell, working in the Jackson Laboratory, Maine, USA, a small, independent non-profit research institution. He discovered a situation in which transplants would be rejected even when they didn’t have non-self proteins.
To understand the mystery – to think about it deeply like Kärre did – we need to consider the genetics of the inbred mice used in Snell’s experiments. Inbred mice are obtained by successive breeding between siblings (or parents and their offspring) over long periods.3 Offspring from two different types of inbred mice are called the F1 hybrid. Not the cutest of baby names, it stands for Filial 1 hybrid and is a widely used genetic term to describe offspring from different strains of animals or plants. For example, a mule is the F1 hybrid of a male donkey and a female horse. That is, a mule came about when a donkey and horse mated rather than being a species that evolved through gradual changes in an ancestor of all three animals.
The importance of inbreeding here is that all the mice from one inbred population have identical compatibility genes – the normal diversity being wiped out by the inbreeding. Usually, there are different compatibility genes on each strand in the double-helix shape of our DNA. On one strand of the helix there are genes inherited from the mother and on the other strand there are genes from the father. This gives us, for example, two versions of the HLA-A gene. But, because inbred strains of mice have the same compatibility genes on each strand of their DNA, there’s no variation in what they pass on to their children. And – crucial to the transplantation mystery – F1 hybrids inherit all of the compatibility genes found in their parents. So F1 hybrids should be able to accept transplanted tissue from either parent.
But here’s the mystery: Snell found this to be true for skin or organs like kidneys – these can be successfully transplanted from parents to an F1 hybrid – but transplants of bone marrow are rejected nonetheless. Why was bone marrow rejected? It’s a violation of the basic rule for transplantation, because the parents’ cells do not have non-self compatibility genes.4 It was a crack in our understanding through which a whole other aspect of our immune system would be uncovered – starting with the discovery of a new type of cell.
In 1971, scientists at the State University of New York, Buffalo, USA, glimpsed that a new immune cell could be responsible for the rejection of bone-marrow transplants.5 They found that mice with their thymus surgically removed would still reject bone marrow. Since T cells need the thymus to develop properly, this indicated that something other than these immune cells was responsible for the transplant rejection. But it took several more years for clearer progress to be made in solving the transplantation mystery. What turned out to be crucial were experiments by scientists tackling an entirely different problem, nothing to do with F1 hybrids or transplantation, but rather with cancer.
During the early to mid-1970s, many teams of researchers across the globe were performing experiments to compare how well diseased cells – such as cancer cells – could be killed by immune cells taken from different people (or different animals). They would test, for example, how well immune cells taken from different patients with leukaemia could kill cancer cells, in comparison with immune cells taken from healthy people. The thinking was that leukaemia patients would have immune cells activated to be efficient killers because of their exposure to leukaemic cells, while immune cells from healthy people should not be able to kill cancer cells – they would serve as the ‘blank’ control sample. But it was often found that immune cells from healthy people could, in fact, kill cancerous cells.
Even more surprising, cancer cells could be killed by a person’s white blood cells even when their T cells – the type of cell everyone thought was responsible for killing cancer cells – were deliberately removed. Most scientists took this as merely an inconvenient ‘background’ killing, likely caused by some inaccuracy in the way that killing was measured. A few people thought that there could be an odd type of T cell left behind after most had been removed. Hardly anybody considered that there could be an altogether new type of cell responsible for killing cancer cells.
Most teams simply ploughed on regardless – trying not to get distracted by the ‘background’ problem. Some researchers found ways to circumvent the issue – by only using blood from donors whose cells happened to be particularly weak at killing the cancer cells being studied. In effect, they were exploiting the diversity in immune responses to get rid of the ‘background’ problem. They set up their experiments so that the results would fit with contemporary ideas about what should happen. It seems erroneous in hindsight, but in fact it’s not that they were being particularly bad scientists; this kind of blinkered view is often necessary. When a computer crashes, who thinks it’s worth spending the rest of the day trying to figure out precisely what happened? We all just swear a bit, try ‘Ctrl + Alt + Delete’ and then just turn the computer off and on again to keep moving. It’s just extremely hard to know when an unexpected result has something important at its root. There’s always a rush to new knowledge – and to get a PhD, next job, or grant – and who’s got the time to hang about wondering why a computer crashed, or why there’s an irritating background signal coming from the blank control?
To realize that something interesting hid in the ‘background’ took a certain attitude. Months or years of hard work could be wasted if some boring technical problem is all that’s uncovered. A scientist’s life isn’t at stake in the same way as when an astronaut accepts the danger of space flight, but you still need something of the right stuff to take on and solve a scientific mystery. The breakthrough that solved the ‘background’ problem – and in turn, the transplantation mystery – came from two pioneers working independently; Ronald Herberman at the US National Cancer Institute and Rolf Kiessling in Stockholm, Sweden.6
In 1970, at the age of twenty-two, Kiessling had begun his doctoral studies at the Karolinska Institute, Stockholm, a renowned hub for studying immune responses to tumours. His plan was to find out how well mouse T cells could kill a particular tumour cell (called YAC-1). It was a fortuitous choice, because YAC-1 is killed especially well by the immune cell responsible for the ‘background’ killing; so the ‘background’ killing was particularly high, harder to ignore. Kiessling realized that the tumour cells were being killed by cells other than T cells and he named them Natural Killer (NK) cells.7 NK cells are, in fact, especially good at attacking cancer cells – and also some types of virus-infected cells. There are about 1,000 of them in every drop of your blood, and each is capable of killing around twelve cancer cells. But after Kiessling published his paper, he saw Herberman’s report on the same new immune cell. So many people participate in modern science that it’s hard for anyone to make an important discovery in the way they dreamed they would – on their own. Rather than being relieved that his findings had been confirmed immediately, Kiessling was frustrated by the competition.8
For a decade, Kiessling continued studying NK cells but then, in the mid-1980s, he decided to change direction entirely. He simply wanted to try another area of research and he wanted to work on something closer to human disease.9 He stopped going to scientific meetings on NK cells and, in 1986, he moved to Ethiopia to work on leprosy (known as Hansen’s disease in the US). He decided that he should study the immune response against the bacteria that cause leprosy, thinking this might indicate a way to vaccinate against the disease. Arguably, it was a bad career move. He had his reputation sealed for ever among scientists studying NK cells and was unknown in the world of leprosy research.10 The irony is that it wouldn’t be long before NK cell research did become relevant to human diseases – as our understanding of these cells deepened. Kiessling has no regrets and says his time in Africa was one of the most exciting periods in his life.11 He could return to conferences about NK cells at any time – where he would be welcomed, revered even – but, talking to me in 2011, he said, ‘I would hate that – turning up like some kind of dinosaur.’12
Shortly before Kiessling left for Africa, in 1985, the other discoverer of NK cells, Herberman, became the founding director of the University of Pittsburgh Cancer Institute.13 He successfully directed the institute for almost twenty-four years but towards the end of his tenure, in 2008, he became the centre of a national controversy when he issued a statement to advise everyone in the Cancer Institute that they should reduce their use of mobile phones. He issued a two-page memorandum which included advice to not allow children to use a mobile – except for emergencies – and to avoid carrying one on your body at all times. The multi-billion-dollar phone industry wasn’t happy; and the furore was reported in national and international newspapers, magazines and on TV news stations. Herberman defended himself, saying that we shouldn’t wait for a definitive study to come out, but should err on the side of caution.14 Though he had published more than 700 scientific papers and discovered nothing less than a new type of cell, his stance on mobile phone use garnered him the most public attention by far.
