Disease Models & Mechanisms 1, 17-19 (2008) doi:10.1242/dmm.000810 A MODEL FOR LIFE

Using to understand folding diseases: an interview with Susan Lindquist

Susan Lindquist is a founding editor of DMM, whose pioneering work in yeast has advanced our understanding of in disease, including Parkinson’s, Huntington’s and diseases. Here, she discusses her personal approach to model organism research and scientific leadership.

rotein shape is vital to its func- of. It’s not just regulated at the level of tran- tion. Pathological processes, such scription, which was the hot thing at the as , stress tol- time; it’s regulated at the level of preferential erance and prion diseases, often translation, selective RNA turnover, selec- result from the misfolding of pro- tive removal of polyadenylation, and prefer- Pteins. Who could have imagined that re- ential transport of RNAs from the nucleus. search carried out in a unicellular organism, We uncovered a whole slew of regulatory such as yeast, would yield discoveries rele- mechanisms and found that they worked in vant to the treatment of complex human an incredibly orchestrated way. That was neurological diseases? Susan Lindquist great, but we didn’t know what the

DMM imagined that this simple eukaryote could were doing. At that point we needed to reveal plenty about protein folding and know what the proteins were doing and ge- pathology, and she was right. netics is a powerful tool for that. As soon as I heard about the new yeast What characteristics led you to focus on methods, I signed up for the Cold Spring yeast as a model organism? Harbor course on yeast. Gerry Fink [who de- the organism are just wonderful for experi- I leapt from working on Drosophila to veloped baker’s yeast as a model for studying mental manipulation. It can grow either as working on yeast literally the moment I the fundamental biology of all organisms and a haploid or a diploid, so you can cover or heard about the technique devised by Terri is a Professor of at MIT and a uncover the effects of any time Orr-Weaver, Jack Szostak and Rod Rothstein. Member at the ] was one you want. It is very easy and cheap to grow. They had figured out how to put a of the teachers. I remember at the time the It has a small , so it wound up being into a piece of DNA and target it back into senior faculty didn’t spend much time advis- the first higher organism to have its genome the genome, replacing the gene in the chro- ing junior faculty. The only time someone sequenced. Another great thing about it is mosome with what you wanted [Orr- did stop by to give me advice was after that it actually does things in an amazing Weaver, T. L., Szostak, J. W. and Rothstein, R. hearing I was going to start working on yeast number of ways, just like human cells do. It J. Yeast transformation: a model system for – three years into my assistant professorship. is a simple, little organism but it has all of the Disease Models & Mechanisms the study of recombination (1981). Proc. He said: “that is ab- cellular compart- Natl. Acad. Sci. USA 78, 6354-6358] [using solutely crazy, don’t My idea is to use the right ments – the endo- yeast as a model organism]. I thought, “Wow! switch organisms, organism for the particular plasmic reticulum, a It is just absolutely fabulous.” don’t do something membrane-bounded We had been working on heat-shock pro- completely different question you are trying to get nucleus, vesicle traf- teins and using them as a system to study right in the middle of at and move around a lot ficking – as well as gene expression, asking ‘how does an or- the tenure clock.” But chromatin structure, ganism rapidly and completely change its I went ahead and decided to do it. (As a transcription factors, specific mechanisms pattern of gene expression in response to a woman, at that time, I hadn’t really thought for regulating the cell cycle, and many dif- specific stimulus?’ We did a lot of satisfying it was likely I would get tenure anyway. So I ferent types of signal transducers. All of these and interesting work at a time when very thought it was too good to pass up.) I’m so work in much the same way as they do in little was known about how organisms can glad I did. That capacity to go in and knock higher organisms. Bacteria do a lot of things control what proteins they will make. We out a gene using site directed mutagenesis quite differently. Don’t get me wrong, bac- found that the expression of heat-shock pro- was just a transforming thing in terms of ex- teria are great to work with, too. They grow teins is regulated at every level you can think perimental elegance. Since then, and indeed even faster! And for studying many truly fun- before then too, many things were done to damental problems in biology they are ter- Susan Lindquist is a Professor at the Massachusetts make the [yeast] organism more manipulat- rific. But there are many layers of biology, Institute of Technology and Whitehead Institute of able. It all started with brewers wanting to and particularly many problems related to Biomedical Research, and an investigator in the Howard Hughes Medical Institute. make better beer about a hundred years ago. specific human disease mechanisms, that (e-mail: [email protected]) But it continued because certain aspects of cannot be studied in bacteria. But in yeast,

Disease Models & Mechanisms 17 A MODEL FOR LIFE Susan Lindquist

protein trafficking – in and out of the homologues. We send [our collaborators] test different combinations of therapeutic nucleus, through the secretory pathway, into expression clones or viruses, which are then strategies initially derived from genetic organelles – the control of growth and divi- cloned into these other systems. [This analysis in yeast, nematodes and rat neurons. sion, responses to diverse stimuli, mito- process] has validated the effects of some of These are the big scheme things that I chondrial respiration, all this is very similar. our genes on toxicity due to α-synuclein. So would like to do and they are enabled by the There are obviously many differences I think this is really exciting – that’s one fact that this pluripotency technology [the between humans and yeast. It goes without billion years of conservation for a basic cell ability to manipulate cells into discrete saying: a yeast cell is not a neuron. But you biological process. mature lineages] has come about. It lets us can study much of basic eukaryotic cell make a wide leap. New imaging techniques biology in yeast. For example, we are study- How do you think recent technical ad- are also fabulous. We have not yet been on ing neurodegenerative diseases. Why would vances, for example genomics, will influ- the forefront of imaging, but I’d like to get anyone think to study a neurodegenerative ence the future model organisms? there. One of my postdocs is attempting disease in yeast? Many of the problems in Technologies are incredibly enabling. some amazing things in collaboration with these diseases derive from problems in Certainly the genome sequencing that has Matt Lang’s group here at MIT. protein folding and trafficking and that is been done has opened up many more or- Another thing that is terrific is the entry largely the same in yeast as it is in neurons. ganisms to study, it’s absolutely tremen- of different types of people into this field. To the extent that the problems are the same dously empowering. Invertebrates, verte- The physicists have brought in all kinds of [between yeast and other organisms] it is brates, and other fungi become powerful interesting ideas in terms of technologies. really great to be able to study it in yeast and you get access to doing things with Engineers too – tissue engineering and mi- because they are so fast to work with and pathogens that were [previously] very diffi- crofabrication – so that you can study because a host of very clever people have cult. I think now we need to develop other processes in parallel in large numbers much created such amazing tools to work with tools to work with these organisms. There more rapidly. Thinking about the circuitry

DMM them. We’ve then been able to move from are many things that you might want to of the cell, engineers bring a whole different yeast into neurons largely through the help study in another organism. For example, [let perspective to it. It’s a phenomenal time for of collaborators, who have been wonderful. us take] a pathogenic organism. We have biology right now and it’s such a shame that It is great having a group of people to inter- been doing some looking at Plasmodium we – and by this I mean the entire scientific act with who have expertise in very different falciparum, one of the organisms that causes community – are so pinched in terms of areas. malaria. It’s very difficult to manipulate ge- funding. netically. It’s hard to grow [and] it has a very How do you approach the great distance complicated life cycle. But there are certain If you were to begin a completely new between a yeast cell and a mammal? aspects of the biology of P. falciparum that project, what would it be? The major way we’ve done it is with collab- one might be able to study by transposing its I would want to tackle the malaria problem orators. With one of the diseases we work proteins into a yeast cell. For example P. fal- I just told you about, because it is such a with, which is Parkinson’s disease, the neu- ciparum has a very weird proteome. It has dreadful disease. And with global warming, ronal cell lines do not seem to be to be very a lot of asparagine-rich proteins in it and I think it is going to get worse. A fresh and good for studying [mechanisms of the many other simple sequence repeat proteins unique inroad into it might be the unusual disease]. I think that neurons are not meant as well. I think this may create a particular nature of its protein folding problems, to have continuous replication and when vulnerability with respect to protein folding because its genome encodes proteins that Disease Models & Mechanisms you have a neuronal cell line in culture that could potentially (this is really a ‘pie in are simply so weird. But whether I will do derived from a tumor, it’s just not really the sky’ thing) lead us to entirely new ther- that or not, I don’t know yet. normal. They’ve lost a lot of their apoptotic apeutic strategies. It happens that my lab What would I get into I if I was really mechanisms. So the neuronal cell lines have knows a lot about protein folding, and es- starting fresh – if I was a postdoc or grad not been as useful as one would hope for pecially about the folding problems of student trying to decide what to do? I find studying some problems. That’s not to say simple sequence proteins. So we are think- that I love so many different aspects of that there are not some fabulous things done ing about taking some of the P. falciparum biology that I would just try to find some- with cell lines! There have been, but some proteins that look like they would have a thing that gets me excited and move out responses to protein misfoldings and mis- hard time folding and putting them into from there. trafficking may actually be more similar in yeast cell to study. Certainly one of the great mysteries and yeast than in cultured tumor cells. In any Another thing that we are thinking about great frontiers is the brain. How does our case we’ve translated some of our yeast find- doing is to work with Rudolf Jaenisch on brain work and store all of our memories? We ings to neuronal models in other ways. For making IPS [induced pluripotent cells] and, have a bit of a toehold on this and are working example, we collaborated with Chris Rochet as we start to unravel some of the genetic on it with and Kausik Si. Crazy as to use differentiated primary neurons taken processes that are causing PD [Parkinson’s it sounds we are actually working on this in from the brains of embryonic rats, and with disease], actually use cells from patients to yeast. This springs from other work we are Guy Caldwell to study dopamineurgic discover what strategies are most appropri- doing on prion biology. The name comes neurons in nematodes. We take genes that ate for that individual. [Since] different pa- from this awful, horrible disease where a we find in yeast to serve as genetic suppres- tients will have different genetic predisposi- protein changes shape and then it creates a sors or enhancers and clone their human tions, we hope to take such cells and try to conformational chain reaction where one

18 dmm.biologists.org Susan Lindquist A MODEL FOR LIFE

protein after another undergoes a change in utation as someone who creates positive his major priorities. In fact he has been able shape. It’s all the same protein but it can have working environments. In your opinion, to do far better than I. The postdocs do feel different shapes. And one of those goes and is there an identifiable infrastructure or that people care about them and that we [the reacts with another protein of the same type type of organization that provides the faculty] remember when we were there. and gets it to change its shape too. It causes most supportive environment for scien- We have a wonderful, long tradition at the a horrible disease by a process we still don’t tific research? Whitehead of a retreat. We go up to New understand. A similar process can occur in I think there are several things [that enable Hampshire for a few days, all of the students, yeast cells, but in that case it doesn’t cause a people to do their best work]. In terms of my all of the postdocs, many of the technicians horrible disease, it just changes the function own laboratory, I have two types of criteria. and, importantly, every single faculty of the protein. Importantly, that change in First, that people be bright and creative and member. There are many places that have re- shape and function perpetuates itself, from rigorous…. Good scientists. But every bit as treats, University of used to have protein to protein. So the change in function important, a very high priority in bringing one and I attended about half the time. Terri is transmitted from one generation to the someone in is knowing that they are gener- Orr-Weaver, when she was away on sabbat- next generation in the yeast cell. You actually ous, open, want to share information, like to ical in Greece, came back for the have a heritable element that is based upon help other people, and are willing and ready [Whitehead] retreat. That kind of commit- a change in protein shape, not a change in to accept advice from other people. People ment to having a community, and realizing nucleic acid. don’t get into my lab anymore unless they that the whole is much greater than the sum It is an interesting mechanism to create a are like that. Still, there are a lot of misun- of its parts, is really important. At our retreat ‘molecular memory’ in a sense, because once derstandings that will happen and I honestly the faculty are there the whole time, talking you change conformation, there is a self-per- think that one of the most important things to people, looking at their posters. It really petuating loop to keep it going. The propa- is to be open about things. I ask people when takes that level of commitment. Last year gated change in shape is associated with a they come into my lab to be [open]. I have a two people in my lab didn’t go, both were

DMM change in function that passes from genera- wonderful lab manager and when someone having babies. Now that is a good reason not tion to generation in yeast. But it is an inter- has a problem they first should talk to her to come. People take it very seriously and esting way to think about how other types of and if it cannot be resolved in an easy way they do so because they know the faculty memory might be encoded – even neuronal then they can come talk to me. I had an does too and that they will be there. memory. Everyone I mentioned this to Italian mother and a Swedish father and While at an institutional level, we cannot thought I was crazy [for this idea of a protein- they were stereotypical in their ways of go around to see how collegial every student derived memory process] until Eric Kandel dealing with the world. They were con- and postdoc is but what we do is make very came into my office and asked: “Do you think stantly misunderstanding each other. I loved careful decisions about our faculty. The might be involved in learning and them both so dearly and I saw them have Whitehead faculty has lunch together every memory.” I nearly fell off my chair. He had a these misunderstandings that were simple Thursday afternoon. We really know each gifted scientist in his lab, Kausik Si, who had and it drove me nuts. I kept having to other, we talk to each other and we interact found a protein that is involved in learning mediate between them when I was a kid and a lot. When we hire a new faculty member, and memory and is located at the end of the I think I still have some of that left in me we are looking for the most brilliant minds synapse. It had sequences on it that looked now. I can understand that people say things we can find but we are also looking for just like our yeast prions. We collaborated in different ways and they just need to get it people that we want to interact with and with them to study its prion-forming capac- out into the open and talk about it. I usually who we think will be part of the community. Disease Models & Mechanisms ity and to try to identify the regions of the find that difficulties that happen in the lab- You really can establish a community by cre- protein that are involved in making its con- oratory are just simple misunderstandings. ating a set of operating principles. formational change. We do see [their protein In terms of institutions, I think some of Another thing that an institution can do, of interest] undergo a conformational change those lessons apply to an institution as well. if they have any financial resources at all to when we look at it in yeast and it also self per- You can’t, as Director of the Whitehead, do it, is to provide seed funding for crazy petuates that change. And that perpetuates screen everyone to see if they are going to be ideas that would be high risk, high payoff a change in function that would be expected good colleagues; that just doesn’t happen. ideas. The Whitehead has a tradition of to help maintain the synapse. You can try to put in place support structures doing that and it is very central to its mission. Now we are looking for other yeast prions that let people know that you really care The DMM staff greatly appreciates Susan and we think that we have found several that about them and you care about creating an Lindquist’s candor in relating her interesting are completely unrelated proteins. The next environment where they can do their best personal story and sharing her insight about phase might be to look for them in other or- work. One of the first things I did when I was creating lab and institutional environments ganisms, such as humans, now that we’ve Whitehead Director was raise the postdoc that enable productive science. Her creative learned how to work with them using a high stipend because I thought it was too low and research demonstrates the value of model or- throughput – or moderately high through- create a system to reward people who got ganisms in understanding and treating put – system in yeast. their own fellowships by giving them a little human disease. We feel that her work and per- extra funding that they could use at their dis- sonal example provide a fitting subject for the You have an unusual breadth of experi- cretion to help support their career. I’m very first ‘Model for Life’ article in this new journal. ence in both high level administrative and happy to say that David Page, who is the Susan Lindquist was interviewed by scientific roles and you have gained a rep- current Director, has taken that on as one of Kristin Kain, Associate Reveiws Editor.

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