In Barcelona

I have finished my stay in Lyon and arrived to Barcelona to attend a round table for young researchers organised by the Universitat Autonoma de Barcelona. Interestingly enough the definition of young researcher seemed to include any researcher after the PhD but without a stable contract (that is, postdocs, non tenured group leaders and people in teaching positions).

I was a rather interesting discussion that dealt with things that I imagine are common worries for young researchers across Europe and elsewhere. Mainly the difficulty of living on short term research contracts, (for those of us postdocing somewhere else) the strain of keeping up with friends, relatives and former colleagues while living abroad, the gap between our real age (late twenties or early thirties) and how our status is perceived by the rest of the population (not like assistant professors or people with “real” jobs and more like students with a fancy “Dr.” in front). Other issues that I found very relevant not only for young researchers are the link between research and teaching (in Spain, like many other countries, university lecturers are paid to teach but their progress on the career ladder depends exclusively on publications) and linked to that if the main duty of academic staff is to perform research or to teach (there seemed to be some consensus that universities should be free to chose wether to have a research profile or a teaching profile).

Lenski et al: Balancing robustness and evolvability

R. Lensi, J. Barrick and C. Ofria. Balancing robustness and evolvability. PLoS Biology, Vol. 4, 12, pp 2190-2193

This paper has not much to do with cancer but I have been interested in evolvability issues for a while so I decided to take a look at it. Tumour evolution has many but not all the features of the evolution involving longer time scales but its evolvability is not a thoroughly investigated topic. That is a shame because it seems that, given enough time, one would expect that tumour cells will not evolve only towards phenotypes that can take better advantage of the environment but also to genotypes that allow evolution to adapt better to that changing environment.

This paper does not explore this but something also interesting: that robustness and evolvability might be desirable but incompatible aims. Robustness can be seen as he ability to counteract change while evolvability represents the capability to adapt. In general it is true that species must strike some sort of compromise between these two abilities since organisms need the robustness provided, for instance, by the DNA repair mechanism but species need mutations that actually allow these organisms to better adapt to the environment. This is not always true and there are cases in which robustness and evolvability can go happily hand by hand. One such case is genomic redundancy. Up to a point, genomic redundancy improves robustness since functionality is kept in more than one location making it less vulnerable but also it helps evolvability since it allows duplicated genes to evolve different functions.

The general rule though is that organisms cannot be entirely robust to change in the form of genetic mutations since such an organism would freeze from an evolutionary point of view and thus subject to become extinct when a fitter rival comes around. I guess that that is a good explanation to cancer, a perfect reproduction mechanism would have not led from simple organisms to humans.

Cancer and biofuels

I have recently commented how (in my particular view, especially at the theoretical level) research in some area can be used in a different one but I guess I did not expect this: Cancer research may help biofuels.

It seems that, inspired by research done at the Fred Hutchinson Cancer Research Center in Seattle, a company called Targeted Growth is doing to corn the opposite of what oncologists do to human cancer cells taking advantage of the fact that some pathways in these two different cells are similar. The idea is to promote plant growth by overriding the genetic clock that tells the cell when to stop growing. The advantage is that plants thus modified are not transgenic (whith the load that this label carries to many consumers) and that it can lower the price of growing them as biofuels and thus promoting them as a good value alternative to oil.

Axelrod et al: Evolution of cooperation among tumor cells

R. Axelrod, D. Axelrod and K. Pienta: Evolution of cooperation among tumor cells. PNAS vol 103, 36, pp. 13474-13479, 2006.

A few months ago a friend of mine from Vienna send me the link to this paper (thanks Peter!) and although I skimmed through it at the time only now did I have the chance to read it with a little bit more of care. Robert Axelrod is well known in the complex systems and game theory communities. The research he did almost a quarter of century ago (detailed in his book: The evolution of cooperation) explained how cooperation can be established between two agents (people, elephants or cells) even when the mechanisms of the cooperation have not been agreed beforehand and the agents could gain more in the short term by not cooperating.

Now Axelrod and coauthors speculate on how this approach could be used to study carcinogenesis. They present this in the framework of Hanahan and Weinberg and the six capabilities required to progress towards cancer (self sufficiency in growth signals, ignoring anti growth signals, evasion of apoptosis, angiogenesis, limitless replicative potential and invasion/metastasis).

Now, this paper is no regular paper. Most research papers I read describe a particular piece of clinical research (we have investigated this gene in this context…), mathematical or computational model (in this paper we introduce a model that explains the influence of acidity in…) or are review papers. This one does not describe new clinical research nor does propose a formal way to describe any aspect of oncology nor represents a review of carcinogenesis research from the cooperation point of view. This is not meant to be a criticism. The paper represents for me a new category of papers, one whose aim is not as much as telling finished research as to suggest to the reader new venues of research under a particular perspective.

If that was indeed the aim then this is a good paper. According to the authors, the conventional view on tumor progression using the Hanahan and Weinberg framework is that cells have to acquire all the six capabilities but under the new cooperation based view this is no longer necessary. It could be possible that, at least some of this capabilities are provided by some cells to others and thus cancer could occur when groups of cells displaying a mixed set of capabilities collaborate to create the same effect of a single cell acquiring all the capabilities and reaching fixation (taking over the tumour population) by clonal expansion. One of the things that I was not very comfortable with is that the authors state that cancers are the result of genetic (or epigenetic) instability. Readers of this site probably know that this is currently a hotly debated topic (something as fundamental such as: what starts carcinogenesis) and that in front of the Weinberg school (cancer starts from genetic instability) is the , say, Tomlison school (a bigger number of cells and selection suffices to explain the start of cancer). My view is that if tumour cells can cooperate in order to share capabilities and progress down the path of carcinogenesis then having a higher mutation rate might not be so relevant and thus a cooperation based view on cancer would favour the view that cancer does not really need genetic instability to get started. If this view of mine turns out to be a stupidity remember that you read it here first.

The paper provides a number of examples of capabilities in which cooperation can happen. In angiogenesis (where cells can produce growth factors that benefit not only the producing cell but others in the neighbourhood), self sufficiency from (certain) growth signals (there is a certain amount of growth signals which can be produced in paracrine or autocrine fashion) and in invasion/metastasis (collaboration to degrade the ExtraCellular Matrix).

The authors point out that this view of carcinogenesis arises a number of new research questions such as what are the resources that can be shared among cooperating tumour cells, what mechanisms are used to share these resources, how does this affect the order in which mutations appear (since mutations can appear in parallel)? Interesting questions but it might take some for someone to come with the answers…if it is that answers can be found using evolutionary cooperation.

Mitochondria and apoptosis

A couple of posts ago I mentioned this research in which RNAi was used to restore the functionality of the mitochondria, especially its role in apoptosis. Now I read that the same results are being obtained by Dr. Michelakis and colleagues at the University of Alberta in Canada using a well known drug, dichloroacetate (DCA).

DCA is an affordable drug that has been previously used to treat metabolic disorders so it is known to be safe and has no patent. What should have been a blessing could also be a curse since there is little incentive to large pharmaceutical companies to finance the clinical trials. The news has been reported in all sorts of news outlets from Cancer Cell to Slashdot and including The Economist. In this website you will be able to find the latest results as well as information on how to donate money so Dr. Michelakis and his group can finance the clinical trials.

Incidentally, in the link pointing to these news in the online version of The New Scientist, a researchers from Dundee mentions something I did not think of at that time. It could be that the metabolism and not genetic mutations spark cancer. Of course for the metabolic switch to take place you will still need hypoxia (low oxygen due to distance to vasculature) which means, if I am not wrong, a neoplasm.

World cancer day

I guess I missed it. It seems that yesterday, 4th of February, was the world day of cancer. As many other “World day of…”, this WOC was one of these events designed to raise awareness of the problem of cancer in the world, although given that cancer is in the top two of the diseases that are responsible for more deaths in the developed world I guess that many people are more than aware of it.

The headlines I am reading sound actually quite optimistic. Death rates are decreasing due to early detection and improved therapies. Of course nobody is suggesting that cancer will be eradicated but that it will become a chronic disease. I am not sure of how much impact has mathematical oncology had on all these successes but I suspect that it has been limited. For one, mathematical oncology is a fairly relative newcomer in the world of oncology and oncology is a discipline in which cutting edge discoveries take many years (or decades) to reach the public. For another one, I think it is highly unlikely that there will ever be headlines of the kind “theoretician cures cancer”. Theoreticians deduce rules or laws that try to describe things like, for instance, cancer growth. These can be used by experimentalists to focus on the more promising areas of research and design the therapies with more likelihood of success faster.

Another added advantage of theoreticians is that they can connect research in different areas. Things that apply to cancer evolution can also be used to study the evolutionary dynamics of other diseases. Many diseases are dangerous due to their capability of evolving and being able to tell what (phenotypes) to expect in the near future from what is there now (genome) would be crucial to deal with them. This week’s issue of science carries a paper (http://www.sciencemag.org/cgi/content/abstract/315/5812/655) about how the H5N1 virus (infamous for the avian flu) suggest that only two mutations stand between the current problem and one in which the virus could affect and spread in humans causing a global pandemic. Is there anything that we know about how a tumour evolves that could be used here? I would not be surprised if the answer turns to be positive.