009 - Chimps, cancer genes and missing kids
Kat: Hello, and welcome to Genetics Unzipped - the Genetics Society podcast with me, Dr Kat Arney. In this episode we bring you a very special interview with Mary-Claire King - one of the world’s leading geneticists, whose work has spanned everything from comparing chimps and humans to finding the first breast cancer gene to reuniting families that have been torn apart.
The 8th of March is a double-whammy in the calendar of days to remember. Not only is it International Women’s day (yes, ladies, we just get the one…) but it’s also International Mendel Day - the anniversary of the day in 1865 that Gregor Mendel presented the final installment of his groundbreaking work on inheritance to his local scientific society in what’s now Brno in the Czech Republic.
So the Genetics Society decided to use the 8th March to bring both of these themes together, hosting a day of talks at the Royal Institution in London in collaboration with the Mendelianum - the museum and research centre in Brno dedicated to Mendel’s life and work. It culminated in a public lecture by leading geneticist Mary-Claire King.
Now the American Cancer Society Professor at the University of Washington in Seattle, Mary-Claire has contributed to many areas of genetic science during a career spanning more than four decades, from her early work showing that human and chimpanzee genes are 99% identical to finding BRCA1, the first ‘breast cancer gene’. Since the ‘80s she has also been putting her genetic skills to use to solve human rights abuses and war crimes all over the world.
I was lucky enough to sit down with her for a fascinating chat about her life and work, starting with the question of what got her interested in science in the first place.
Mary-Claire: I was interested in math before I was interested in biology, way before. I became interested in math because when I was very small, my dad was already home. My dad was born in 1890, so he was a full generation older than most dads, and he was already largely bedridden by the time I was five, six years old, so he was home. And that was early in the days of television. One of the very first things to be shown on television were baseball games. So my dad and I would watch baseball games together, and he would make up story problems for me.
Here's a baseball story problem – and this is for the American listener - Ernie Banks is up, he's batting for the Cubs. His batting average is .277. My dad would say, "Suppose he's going to be up three times in this game, how many hits is he going to need to hit out of those three, to make his batting average go to .280?" And I was six, yeah? And I would listen and I would say, "I don't know." And he would say, "You're right! You don’t know. What more information do you need in order to be able to figure it out?". And the answer of course is you need to know how many at bats he's had already.
So the idea of working out story problems while watching baseball seemed to me perfectly natural and the way everyone watched baseball - I wasn't fully aware of how most baseball watching was done.
Kat: It's like Darwin's children saying, "Where does your daddy do his barnacles?"
Mary-Claire: Yes, that's right. So the idea of story problems was never foreign to me, was never threatening to me. And as I grew up, I just liked story problems, and of course maths is basically story problems, proofs are basically story problems. I did maths as an undergraduate, but it was clear to me - because my younger brother was much, much better at maths than I was - that there was no way I was going to be able to be a professional mathematician.
So for graduate school I went to Berkeley. I went thinking I would do statistics, more tractable than basic maths. Got to Berkeley and just for fun, took the genetics course from Curt Stern - the last time he taught before he retired.
Kat: Oh, wow!
Mary-Claire: Right? So I just fell in love with it. I thought; imagine getting paid to do this. This is story problems made relevant and critical for life.
Kat: Made flesh!
Mary-Claire: Made flesh, exactly. Made flesh in a wide variety of different species, some without even flesh, right? So I transferred from statistics to genetics and have never looked back.
Kat: And then when you started thinking about genetics as a scientist, what was your first problem that you addressed then, once you started going into this world of genetics?
Mary-Claire: Right. I was interested from the beginning in the idea of variation and evolution, and how one could understand evolution on the basis of the basic ways that species change. So we have mutation, selection, migration and drift. And those are the four evolutionary processes by which species change.
I thought; how can we understand, from the variation that we see in a species, those processes? This was in the mid-1960s. So the idea of doing protein electrophoresis was just getting of the ground. We weren't yet working with DNA.
At first I thought I might be able to get a grip on that by working with bacterial species, by working on problems in bacterial evolution. It didn't work, both because I didn't have good enough hands - I had, of course, come out of math. I had no background in experimental work at all - and because the electrophoretic methods of the time were not sufficiently precise to be able to see small degrees of electrophoretic mobility difference. They were just coming on and I wasn't nearly good enough technologically to make those advances myself.
Kat: So the really tiny differences you might want to see, you just couldn't resolve them?
Mary-Claire: You could resolve them, but they would resolve differently in different experiments day by day. It was largely because we were doing electrophoresis - it sounds ridiculous in retrospect, but we were doing electrophoresis either in tiny tubes or not-quite-standardised gels. So the resolution was good, but it was not exactly reproduceable.
Kat: So bacteria were a bit of a bust, and then where did you turn your attention in search of some answers, as to how these evolutionary processes might work?
Mary-Claire: Well, this was Berkeley in the 1960s, so there was a lot happening.
Kat: I'll bet!
Mary-Claire: And so I got very discouraged with it. On the one hand I got personally discouraged and on the other hand, the gentleman I was working for, Doctor Stanier, Roger Stanier, moved to France in 1968. He got very discouraged with working at Berkeley and at about that same time, Ralph Nader came to California to work on what became the California Project - Who owns the land of California and what are they doing with it? And he hired me as the biologist on that project.
So for quite a while, for a number of months, I wasn't a student, I worked for Ralph and got very involved in issues like farmworker safety, the completely different issue of forced practices. I wasn't in a lab, wasn't in school.
Then Ralph Nader said, at the end of that project, "Why don't you come back to Washington DC? I'm going to set up what became PIRG and work there. We want to do the same thing with congress that we've done about California." What's happening in US Congress? Who owns congress, right? I was going to do it and I talked to my informal adviser, Allan Wilson, who wasn't my official adviser. Allan said something really incredibly helpful.
He said, "It would be much wiser to finish your PhD." And I said, "But none of my experiments work." He said, "If people whose experiments didn't work stopped doing science, nobody would be left doing science."
Kat: Oh, yeah.
Mary-Claire: Right? And he said, "Perhaps we can figure out a way to design a project for you that will take advantage of the fact that you like to write equations, and that won't require as much technical tour-de-force as the project did in the Stanier lab."
And I said, "So, tell me why it's so critical that I have a PhD. And he said, well if you go now to Washington DC and you work on the project, there's no question it's righteous work, it's a great project. But if you do this with a bachelor's degree, you'll never control the agenda. And if you want to control the agenda in whatever it is you do, you need to have an advanced degree in that area."
It was incredibly good advice. It just made me feel that I wasn't the only one who was having trouble, and that it's really important to have an advanced degree. It was completely outside of my family's history, and indeed it was outside of Allan Wilson's family's history, but he understood exactly the issues. So that's where the project on human and chimpanzee evolution came from.
The idea was - of course by then this was a couple of years later. So the methods of comparing species were more tractable. And it turned out to be a fairly technical project after all. But you know how these things happen, right?
It was a completely different atmosphere in the Wilson lab. The Wilson lab was a remarkable place. Allan died of leukaemia in his 50's. it was just horrible. But this was when he was - gosh, in retrospect Allan must have been in his mid-40's when I was working with him. Over Allan's career his lab had 50 percent women, 50 percent men, which for the time was amazing. I mean, that was probably 90 percent of the women in biochemistry or genetics, that were in the Wilson lab. And it was just a completely egalitarian place. There was a great deal of criticism within the lab of each other's work, but outside of the lab there was complete loyalty to the lab. I loved it.
The project on the degree of distinction between human and chimpanzee proteins, what we would now call DNA coding sequences, was a straightforward project that allowed me to do a little bit of math, to develop a little bit of evolutionary theory. And it led to this result that at first, of course, I thought was my failure to find any differences, because here were humans and chimpanzees looking exactly the same, almost.
I thought; this is just that I can't resolve it, it's got to be me. But there were the occasional, very occasional proteins where there were differences, so I thought it's not completely me, sometimes these actually do resolve. And after I'd been working on this for, I don't know, a couple of years, Allan said, "Have you considered the possibility you've done it all properly and that there really are not differences between humans and chimpanzees?" So I said, "Well, actually, no I hadn't considered that as a possibility at all."
Kat: So, maybe you have done it right after all, and we are basically just naked apes?
Mary-Claire: Yes, exactly right. So we're scaled down, except that we're not. Anatomically, two subspecies of mice are virtually indistinguishable. The bone lengths are relatively, almost identical. Whereas humans and chimpanzees obviously, even a complete lay-person can see the difference.
Kat: Yes, I think I could nail that.
Mary-Claire: Yes, right. So that led us to this idea of - if the protein sequences are so similar and yet the morphological differences and the behavioural differences are so great, we still have this contrast, we still have the difference between the molecules on the one hand, and the morphology on the other. So how can this be? And that led us to the hypothesis that the difference between humans and chimpanzees morphologically and behaviourally and so on, might be due not to the protein sequences themselves, but to their timing and locale of expression.
Kat: I like to think of this as the “it's not what you've got, it's what you do with it that counts” model.
Mary-Claire: That's right, exactly. And when and where you do what you do. It's not what you have. So we postulated that. At the time, this was 1975 by the time it was published and we weren't in a position to be able to test it directly. By the time it was directly testable with the human and chimpanzees genome sequences, Allan had died. On the one hand he was vindicated. On the other hand, he knew he was right. Or he knew we were right.
It was a real partnership and it was the kind of partnership that I have tried to have with students ever since. I will never be as good a mentor as Allan was, but the idea of working with data that really is good data and developing around it a hypothesis that makes sense in an evolutionary context about a problem that's important. I do the same thing now, but I'm now interested primarily in serious illness and disease phenotypes. But it's the same idea.
Kat: I did love that what kind of led out from that feeling was almost like the control switches that turn genes on and off, they are evolution’s playground. You know, you don't want to mess with your genes too much, because proteins do important things. But boy, you can play with the switches.
Mary-Claire: Sure. And the idea that the more complex an organism, the more different ways you have to exploit the same protein sequence, both in terms of their being multiple different transcripts, and in terms of when those transcripts are expressed and in the placement of expression of those transcripts.
This of course also has huge implications for disease, because one form of dysregulation, for example of a gene that may be important in development of brain, could lead to autism. Another dysregulation could lead to schizophrenia. And each of these genes has its own extraordinarily complex profile of regulatory sites, which we are just now beginning to learn what are.
Kat: It’s an interesting comparison with if you have something very simple for telling the time like an egg-timer, you can only break that in so many ways, but if you have a Swiss watch with lots of different parts and different ways of doing it, then that can break in all kinds of wonderful ways and it explains why disease is such a complicated genetic problem.
Mary-Claire: I particularly like that analogy because the idea of the Swiss watch is that it can be dysregulated and so the timing can be a little off without the watch being smashed. And if the watch is smashed, that's fatal. But if it's just a little bit off, because a wire is bent a little bit incorrectly or because a little bit of dust has gotten in, an environmental problem, that can lead to a very serious illness that is the consequence of that dysregulation.
And we see that with serious mental illness. We see that one gene that is dysregulated can lead to autism. A different gene that is dysregulated in a different way can lead to schizophrenia. And there's of course thousands of such genes, so any one of them dysregulated can lead to mental illness without being lethal.
It's fascinating, now that we have the tools, to be able to work this out. I like to think that genetics is a way of thinking that now goes back, well, without the word being applied to it, goes back thousands and thousands of years - as long as people have been thinking about human history. But actively thinking about genetics, what we understand to be genetics, goes back a hundred and fifty years. Now we have the tools to answer the questions we've been asking all that time. So genomics is the set of tools that allows us to address these really ancient questions.
Kat: Later that evening in the Royal Institution’s famous red lecture theatre, we all sat and listened to Mary-Claire talk about the hunt for BRCA1, the first so-called ‘breast cancer gene’, and the implications for women and their families of carrying a faulty copy, which significantly increases the risk of breast and ovarian cancer.
She traced a fascinating journey from the observations of 19th century French surgeon Paul Broca, who noticed that his own wife’s family was affected by many cases of breast cancer, through her own mathematical calculations showing that she would have more luck finding the elusive gene if she focused her efforts on women who developed the disease at an unusually young age, and finally her work to develop a genetic testing panel to help people discover their own risk.
What she didn’t talk about is the story of the bittersweet week in 1981 that set the scene for that discovery, which she tells with tremendous humour in a podcast from the Moth.
Rather than focus on that aspect of her work, I wanted to find out more about the story behind her involvement in using genetics to solve murder cases and reunite families, tackling some of the most tragic human rights abuses and war crimes of the 20th century, starting with the children who had vanished under the Argentinian dictatorship in the 1970s. Apologies for the slight background noise in this part of the interview as the Royal Institution staff start getting the coffee cups ready for the teabreak.
Mary-Claire: I got brought into the use of genetics to investigate human rights abuses by the Grandmothers of Plaza de Mayo in Argentina. The Grandmothers formed themselves in 1977 in response to the disappearance of their adult children and their either infant or in utero grandchildren. They were aware that their children were disappeared and they began to learn bit by bit in the 1970s and early 1980s of small children who were still alive and showing up in households where there had not been anyone pregnant.
They collected this information very systematically and realised as the years went on during the Argentinian dictatorship of the 1970s and early 1980s, that genetics could be a way for them to figure out who was who - to figure out who these children were that had apparently been kidnapped after birth, or born in captivity and kept in military households, sold to collaborators of the military, one way or another were in the hands of people who were involved with the military.
So through friends of friends, they learned of me, I learned of them. I had taught in South America in the 1970s, so I was accustomed to teaching in Latin America. They first asked Luca Cavalli-Sforza, one of the great human geneticists, to help them to develop this statistical approach to addressing that question - the question being, if we identify a child that we believe might be among the children who were either born in captivity to a young woman who has since been killed, or was kidnapped as a prelingual infant with his or her parents, and the parents then killed - can we, by having a sample of blood from that child and from grandparents, determine who that child is? So, paternity testing, but re-applied to grand-paternity testing.
And Luca and several of us worked that out as a straightforward Bayesian statistical problem. And the grandmothers' immediate response was, good, come to Buenos Aires and operationalise it, and Luca asked me to do that and I was happy to do it. This was immediately after the fall of the military, after the failure of the Malvinas Falkland's war, that the Argentinian military of course initiated to try to distract attention from their problems at home and cost the lives of a large number of young Argentinian soldiers, and of course was a disaster.
But they did have to withdraw after, and in consequence an election was held. Raúl Alfonsín, who was a human rights lawyer, became president and established a commission on the disappearance of persons. I was a consultant to that commission and I went to work with the grandmothers on how to operationalise the idea of grand-paternity testing. The grandmothers had collected already 145 case records of children who had been seen at least once alive, whose parents had disappeared.
Kat: This was around 1984 - a time before the DNA fingerprinting techniques that are commonplace today had been developed. So Mary-Claire and her team had to use a technique called HLA typing, which was already being used to match organ donors with recipients based on the similarity of certain molecules produced by the immune system. These HLA molecules vary a lot between people, so finding strong similarities in blood samples between grandparents and kidnapped children proved to be a useful tool for matching up the families that had been torn apart.
Mary-Claire: So we began work, we carried out some identifications of children. We took those cases to court, we were successful and with that success, over the first nine months, a year, came the realisation that there were an enormous number of these cases. And that it was not going to be feasible for all of them to have a solution that was HLA based. There were both logistic and genetic realities. The genetic reality was that one either needed to have or be able to reconstruct the HLA types of all four grandparents. If they weren't all living and they frequently were not, how were you going to do it? Logistically, to actually work out HLA antigen types, one needed to have fresh blood worked on immediately. So, all these challenges.
By this time it was 1985, 1986. I was going back and forth from Berkeley to Buenos Aires working on the problem. And it was exactly the time that the polymerase chain reaction was being developed by my friend Kary Mullis. Kary had been a graduate student in biochemistry when I was a graduate student in genetics, so we knew each other.
He was already working for a company but he was in and out of the Wilson lab. I was still in and out of the Wilson lab, even though my faculty job was in a different department. So I knew about PCR, polymerase chain reaction, within days of it first being developed. I mean, back in the days when we would move tubes from one water bath to another water bath to another.
Kat: Oh, old school.
Mary-Claire: Old school, really old school! And it made it possible to work with sequences - of course, all sequencing was by hand. Literally base pair by base pair by hand, without having a massive amount of DNA from the person. So Allan Wilson was already using this approach to work out human evolutionary trees. He was sequencing part of the mitochondrial DNA genome.
Kat: Mitochondria are the ‘power stations’ inside all our cells, responsible for providing the energy for life. They contain their own little package of DNA that is highly variable between people, and can be detected by using PCR, which makes many copies of a particular piece of DNA so it can be detected and analysed.
Importantly for Mary-Claire’s work reuniting families, virtually all the mitochondria in a person’s body come from their mother, as egg cells are packed with them while sperm don’t bring any of their own. So if the researchers had a blood sample from granny, then they should be able to tell whether an unidentified boy or girl was their grandchild, even without having a sample from mum, as the same mitochondria have passed from grandmother to mother to child. In fact, it wasn’t just granny’s mitochondrial DNA that could provide the key to identifying these kids.
Mary-Claire: It could be a maternal grandmother, it could be a maternal grandmother's sibling. It could be any relative connected only through females. The relative could be male or female but you could have a little boy that you were trying to identify, but if you had the maternal grandmother of that little boy, you could sequence him and you could sequence her and a match was highly meaningful.
Allan, bless him, had already worked out how much variability there was in this particular region of the mitochondrial genome of interest, because he was interested in it for evolutionary purposes. So we were able to take advantage of all that information to sequence hundreds and hundreds of people whose identities were not in dispute in Argentina, in order to get a sense of what the background variation would look like, and to put into application the use of mitochondrial DNA sequencing to establish maternal relationships very quickly. Of course, now it's routinely used in forensics worldwide, but it was the first application, all done by hand, and it works.
Genetics is very powerful and like anything else that's powerful, you can use it for good or you can use it for ill. In this case we were able to use it for very good purposes. I was soon asked to help in the identification of remains because with the polymerase chain reaction, one needed to have only a very, very small amount of DNA in order to amplify and have more.
So we were able to identify remains of people who had been killed by the military by working with DNA from their teeth. If the tooth is intact, you can think of the tooth like a diamond and you can cleave it under sterile conditions, cleave it the way you would cleave a diamond - we actually use diamond cleavers - take out the pulp and use that pulp as a source of DNA for the remains, and identify the person by comparing their mitochondrial sequence to the mitochondrial sequence of people who've lost relatives to the military
So, once we established that principle in Argentina, it became very useful for identifying remains of persons who had been victims of human rights abuses or of wars worldwide. We began to work with our American military to identify soldiers who had gone missing in Vietnam. At the time of the Cambodian invasion there was a journalist who had gone missing, Welles Hangan, whom we were able to identify. Soldiers who had gone missing during World War II, during intervening conflicts in Europe. We were involved in identifying the bones from Ekaterinburg, the Czar and the Czarina, their children and the physician, his family. It's very powerful as long as you know the background sequences, and it's still used.
Kat: Looking back over your incredible career, all the things that you've been involved in, from comparing humans and chimps, finding genes that are involved in breast cancer, the work that you're doing to give people closure about their relatives, it must be thousands of people that you've helped. How do you feel about using genetics to solve these stories?
Mary-Claire: I feel like I've been incredibly fortunate. Genetics is just the most exciting possible thing to do. And I managed to stumble into it at a time when it was just flowering, when it was just opening up. The buds were just beginning to open. The kinds of technologies that allow us to address questions that have been really important human questions since there have been people, are now tractable. They are tractable for the first time, and my generation of geneticists are the people who are able to approach them. Imagine what Mendel would have done with the tools we have now! All we can do is try to emulate his way of thinking, and to take advantage of technology.
Kat: From solving baseball story problems to solving human story problems, thanks very much to the wonderful Mary-Claire King for taking the time to speak with me. We’ll have more from the joint Genetics Society and Mendelianum meeting in a future podcast asking the question, “if Darwin and Mendel had been on Twitter, where would we be now?”
Parallel flight paths
Kat: How predictable is evolution? The question of what would happen if we ran the tape again is one of the biggest questions in modern day biology, and until recently it seemed unanswerable. However, the growing number of known cases of parallel or convergent evolution—where two closely related organism adapt to an environment in the same way—is revealing just how repeatable and predictable evolution can be.
In the latest podcast from Heredity, the journal of The Genetics Society, Dr Allie Graham from Oregon State University and Dr Kevin McCracken at the University of Miami chat to James Burgon about their recent work looking at the convergent evolution of three species of South American ducks to low oxygen, high altitude environments - and, curiously, the ducks seem to have adapted to these breathless heights in the same way that humans have. Here’s James and Allie to give you a teaser.
James: These ducks aren’t the only organisms that we know of to have adapted to high altitude, so how do your results compare to similar ones conducted in other species, and what is your study contributing to our overall understanding of animal adaptation to high altitudes?
Allie: There’s been a number of studies in various human populations, but some of the genes that pop out the most often across Indian and Tibetan and Ethiopian high altitude populations are EGLN and EPAS, for the most part. So seeing that same parallel there was pretty striking. I think more than anything it’s just how predictable evolution can be – I still find it pretty amazing that these continue to be hotspots for natural selection to occur on across a whole bunch of differently-related organisms.
Kat: You can hear the full interview in the latest Heredity podcast.
That’s all for now. In next fortnight’s episode we’ll be telling the stories of some of the overlooked women in 20th century genetics, so make sure you’re subscribed through Apple podcasts or your podcast app of choice to make sure you don’t miss out.
For more information about this podcast including show notes, transcripts, links, references and everything else head over to geneticsunzipped.com You can find us on Twitter @geneticsunzip or email us at firstname.lastname@example.org with any questions and feedback.
Genetics Unzipped is presented by me, Kat Arney, and produced by First Create the Media for the Genetics Society - one of the oldest learned societies in the world dedicated to supporting and promoting the research, teaching and application of genetics. You can find out more and apply to join at genetics.org.uk Our theme music was composed by Dan Pollard, and the logo was designed by James Mayall. Thanks to Hannah Varrall for production, thank you for listening, and until next time, goodbye.
Transcript by Viv Andrews
References and further reading