Stem Cells in Developmental Biology: a debate at the BSDB

Last week the BSDB (British Society for Developmental Biology) celebrated its annual gathering at Warwick. Always a good place to go for quality developmental biology which is enhanced by the arrangement of holding the meeting together with the BSCB (British Society for Cell Biology): these days there is much cell biology in developmental biology. One of the BSDB sessions focused on Stem Cells and highlighted the clear connection between this area of research and developmental biology, or so it seems to some of us but ……perhaps not all.

The AGM of the BSDB had, for the second year running, a ballot to change the name of the society to include “stem cells’ in its name. Thus, the proposal was to change the name from “British Society of Developmental Biology” to “British Society of Developmental and Stem Cell Biology”. The proposal had been flagged last year and, after a vigorous discussion, was rejected, but by a narrow margin which allowed the subject to be brought up again to the AGM this year, where it was resoundingly rejected. But read on……….

The discussion preceding the vote was heated and highlighted several misconceptions about research in stem cells which, perhaps, represent some reality.

The ones in favour argued, correctly I think (I was and am in favour of the change) that Stem Cell research is part of developmental biology and that while there is much that has to do with medicine, the links between Developmental and Stem Cell Biology are strong and essential for both fields, that Developmental Biology can bring rigour and direction to Stem Cell Biology and that Stem Cell Biology can bring challenges, new ways and possibilities for Developmental Biology. They (we) argued that, after all, Stem Cell biology has always been part of Developmental Biology, albeit somewhat cryptically. Including Stem Cells in the name of the society is an acknowledgement of the times and can have its benefits because there is no denying that Stem Cell Biology is a central and key element of research these days; including it explicitly in the Society’s agenda would allow the BSDB to have a strong voice in policy, funding and education in these increasingly influential area of research.

The ones against the change argued that Stem Cell Biology is different from Developmental Biology, that it has a clinical slant which would attract a different crowd to the meeting, force different content in sessions and, overall, distract us from the main business: the workings and evolution of embryos and systems. It was suggested that such a change would alienate several established constituencies within the society that would abandon the group. More significantly, that, eventually, with another vote a few years down the line, Developmental Biology would be booted out of the title for the society to become the British Society for Stem Cell Biology.

As far as a I am concerned this was a missed opportunity. While I appreciate many of the points made by the ‘noes’ , I feel that their arguments are based on fear for a future that will always take over no matter what we do and that, in the long term, there will be consequences from not seeing this. We live in an increasingly corporate world in which lobbies are important and, in the context of our business, provide the basis for funding and policy. For the Society of Developmental Biology Society to have an explicit voice in the Stem Cell community is not just an extension of its natural remit and interests, but it is a way to bring some real science into a field that is increasingly interested in applications without having covered the bases. The foundations of Stem Cell Biology lie in Developmental Biology and it is important that developmental biologists have a say on decision making in that important field. Stem Cell Biology is not exactly, as some people claim, a new area of research (developmental biologists have been working with stem cells and their lineages for years) but it is certainly an area that recently has come of age to carve its own intellectual niche like, in many ways, Developmental Biology did in the 1970s (let us not forget that Developmental Biology is an offshoot of Embryology). It was argued that Stem Cells are born with Till and McCulloch (1964 Proc Nat Acad Sci. 51, 29–36). True but what they were looking at is the question of the origin of the blood, a problem in Developmental Biology whether one likes it or not. At certain places, and stem cell research is one of them, boundaries blur. Is genomics and bioinformatics genetics? Yes it is. In my book, Stem Cell Biology is part, and a very important part of Developmental Biology.

But let us move away from the heart of the question (of course the scientific content) and look, briefly, to the context of the discussion. The boundary, as I have said is blurred, and a situation can develop (and in certain places is happening) that some people, funding bodies, society, come to see Developmental Biology through the eyes of an unbridled Stem Cell Biology. After all, is it not organs out of cells that is the goal of stem cell biology? And is it not understanding these processes the goal of Developmental Biology? Then, what is the difference? The answer is simple, Stem Cell Biology wants to do, Developmental Biology wants to understand. It would be a pity not to bring them together. One can see here history trying to repeat itself: throughout the XVIII and XIX century engineers and inventors were making steam engines with little knowledge of physics, and they worked, but it is when the knowledge of thermodynamics is brought into the framework of the engineers that the engines become efficient. The same can be said of computing where, again, it is physics that makes the hardware that we have today. The fundamental science will always help the more applied side and needs it. So, much to be gained from Developmental Biology having a say in Stem Cell Biology. But there is a second more difficult question: what will be the consequences of the agenda of stem cells running that of developmental biology?

I can see a marginalization of model organisms and a biasing of the agenda towards applied science, applied in a trial and error way, rather than in the tradition of Science. I might be wrong in the extreme formulation of these concerns but I am certain that some of this will happen.

In the end, my impression was that the ‘noes’ were afraid, afraid of the future without realizing that he future will happen and that by not seeing the trends and joining them, we shall always be left to mercy of those trends, without a voice to influence them. I worry that model systems that have taught us so much about basic biology will slowly be squeezed into corners because we do not have a voice to explain that flies have stem cells, that stem cells are part of the make up of an organism which cannot be understood outside its context, that stem cells are a problem of evolutionary biology, that stem cells are a linguistic twist of lineage analysis and lineage analysis has always been a problem of developmental biology, from Roux and Driesch to Garcia Bellido with Till and McCulloch in the middle. Incorporating Stem Cell Biology in the name of the society would have been a way of having a strong voice in a trend that is rapidly gaining momentum.

We shall see what the future harbours. The BSDB is a strong society which represents a vibrant and engaging community so there is no reason why things will change rapidly. However, one thing is clear: there is a need for the voice of developmental biologists to be heard in the Stem Cell community. A mechanism needs to be found for this. It is necessary as much to have a representation to remind that community where their real roots lie and the benefits of listening to the fundamentals of their field. There is a drift which was, unfortunately, at the heart of many of the speeches for the no, that Stem Cell Biology is more clinically than basic research orientated. One can see how this can be construed but, decisions like the one we have taken will increase this gap and foster this misunderstanding. It would be good (it is always good) to take lessons from history. As the interactions between physics and engineering prove, there is much to be gained from the interactions between a field that tries to find practical solutions and one that explain the causes of the problems. Let us hope that the BSDB can find a way to influence some of the directions of Stem Cell biology. For the moment it is as if two twins have been separated; each with their own mind but with shared genetics.

On epistasis, or how genetic analysis can mislead us about biological processes.

As I am about to embark on my brief lecturing stint in the department, thoughts about the subject matter come to mind. One that always concerns me is the value of epistasis (the exercise to create functional hierarchies of genes through the analysis of the phenotypes of double mutants) to learn about processes in developmental biology.

The problem is simple. Genetics is to Biology what mathematics is to Physics: a formal language that allows us to pose questions and find answers. A mutant screen is, in many ways, the formulation of a problem: what controls the decision of a bacterium to use glucose or galactose? What determines the polarity of an embryo? How does a cell orient iself in space? What we find is a collection of mutants which, through some use of our experience (and the rules of genetic analysis), we relate to particular genes. Today, thanks to advances in genomics and the accumulated knowledge of molecular biology, we learn quickly about the kind of proteins that the genes encode and we can weave one of those “Just so stories” that HIF (High Impact Factor) journals like so much: how the gene X affects the nose of the mouse, how the chicken got its wings, or how a neuron lost its way on the way to a muscle……in any event, an important element of the story is to weave the genes together into a “functional network”.  If the story is good it will be bought by a HIF journal and you will have a grant, a job, etc….Now, an important element of the story is the formulation o the relationship between the genes that relies on the analysis of double (and some times triple) mutants: epistasis.

When considering a regulatory process, epistasis allows us to create a linear chain of relationships between the elements (mutants) of the screen for pairwise interactions. The mechanics of epistasis is simple. It requires that the mutants under study (say A and B) have different phenotypes and then asks what is the phenotype of the double mutant (A, B). If the phenotype is B, this means that B is downstream of A i.e. A->B. If the phenotype is A, it is the other way around and A is downstream of B (B->A). If we now can do this with B and a new mutant C, we can construct an A->B->C chain and continue forward.

NB. This is fine in the abstract genetic world of phenotypes since, as those who grew up in metabolism know, when dealing with metabolic pathways, the reverse is true. Suppose you have two steps in which enzyme A catalyzes the change of X into Y, and then enzyme B catalyzes the change of Y into W; if A is mutant the reactions will accumulate Y and the action of B will be redundant i.e. in a metabolic pathway if the double mutant AB is A it means that B is downstream of A!!!! This difference highlights something interesting and perhaps deep about what it is that we measure with mutation; why the difference in this formal language between biochemistry and signalling? There are other uses of epistasis (see Phillips, P. (2008) Epistasis: the essential role of gene interactions in the structure and evolution of genetic systems. Nature Rev. Genet. 9, 855-867). 

Leaving aside terminological issues, there are several problems with the use of epistasis as a way to uncover the functional structure of a biological system, which should make us concerned. Here I would like to highlight three:

1. Machines do not have linear blueprints. The physiology of cells (and this broadly speaking encompasses the sum of the processes that allow them to survive, interact. process information and reproduce) is operated through molecular machines which are often multicomponent. What counts is the operation of these machines as wholes and this does not emerge from a functional linear arrangement of their component parts. I am sure that being clever one could make an epistasis of the ribosome; but this is nonsensical, as what matters is its function as one piece, not our interpretation of its function as the result of a nonexistent array of linear instructions.

2. Feedbacks create problems of interpretation. Feedbacks and time series, create loops in linear systems which can complicate the analysis of epistasis. For example, imagine a ligand X for a signalling pathway Y and a second ligand Z for a second pathway W. It could be that X activates Y which leads to the expression of Z and the activation of W. Epistasis would easily show that X/Y is upstream of Z/W but if now W activation leads to the expression of X (of course now X would act in a different context), we would have a problem for epistasis as X is both up and downstream of Z/W and the genetics could become very confusing. If to this scenario we add the possibility of a feedback of Z/W onto X/Y, the situation that we extract from the genetics would not be simple and certainly not informative.

3. Double mutants are misleading. The reason for this is simple, in a double mutant AB one is not removing two genes from one organism, but rather one is removing gene A from mutant B, or gene B from mutant A; and which one is not possible to gauge. The problem is that, independently of the system, what we are doing in a double mutant is to study the response of a new situation; the loss of B in an A mutant, or the loss of A in a B mutant i.e the reaction of an established and adapted genetic system (the single mutant), one we know little about, to the loss of a gene. This is an important point which deserves some consideration.

These are serious flaws in an analytical tool that is so widely used, and all of them need to be considered when interpreting genetic data. Single mutants are simple to read but even these, sometimes, can become obscure. What can be done?

There are no bad tools, there are bad uses of tools. You cannot cut steak with spoon, nor eat soup with a knife, at least not effectively. It is important to know the limitations of our tools and this is something we should do with epistasis. It can be useful and, indeed, sometimes double mutants are informative, particularly of one is close to a molecular understanding. For example, if a mutant for MAP Kinase is epistatic with a mutant for MEK (the MAP Kinase Kinase) or a Receptor Tyrosine Kinase Receptor (RTK) -in particular if these are activated- we can put our money that MAPK is downstream of both (and this is indeed the case), and built a pathway: RTK->MEK->MAPK which tells us something useful about the system. But, as in the case of the ribosome, there is little use in trying to work out a linear pathway in the dynamics of actin polymerization and we should think more carefully about double mutants.

Final comment: High throughput genetics has brought up a high throughput version of epistasis. Some studies have looked for synthetic lethal phenotypes which reveal that the % of lethal mutant phenotype is higher in double/synthetic mutants than in single mutants. About 16% of single mutants are lethal (Tong, A. H. Y. et al. 2004 Global mapping of the yeast genetic interaction network. Science 303, 808–813) whereas, surprisingly, example in a screen targeted to genes required for chromosome segregation, out of 230 interactions between otherwise viable mutants, 18% (42) were synthetic lethal (Measday et al. (2005) Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation. Proc Nat Acad Sci 102, 13956-13961). Other studies have corroborated these figures and provide a basis to think about QTLs and human multigenic disease (see Phillips above for a discussion of these matters).

Epistasis is about interactions and, as what we want is to uncover function, we should be careful in the way we interpret them. Particularly in these screens, whether they tell us about the ways to break the system when it is weakened or whether they are telling us something about how the system works. My money would be on the first and on the message that this contains: biological systems are redundant, highly connected networks, with multiple backups (see for example Guet et al.  (2002) Combinatorial synthesis of genetic networks. Science 296, 1466-1470). Epistasis is a tool, and it needs to be complemented by many others when trying to infer the workings of the system. Some people call these secondary screens.