Monday, October 21, 2013

A new pre-print server for biology: the bioRxiv

I've written a few posts in the past about the need for a pre-print server in biology, like the one that physics and maths have, in the arXiv, to speed up the rate of dissemination of information in science, and to help promote open access.  As a physicist by original training, posting my work before it is accepted or done has never seemed like a big deal - it is science after all, we're all wrong, all the time (but we're trying to get closer to the truth, AS A GROUP).

In my community, the theoretical (mathematical) oncology community, we have been able to get around the lack of a standard pre-print server as there is a quant-bio section to the current arXiv, but it is certainly not widely read, nor is it really what the folks at the arXiv want to support (but we thank them for doing so, mind you).  In fact, I once tried to get them to add a theoretical oncology section without success - prompting me to create Warburg's Lens - a discussion forum for pre-prints in math oncology.

With the advent of +PeerJ there has been at least one option, and another called CancerCommons has sprung up as well.  In the next several weeks, we'll have another option, the bioRxiv - run by the folks at Cold Spring Harbor - a highly respected biological institute in New York.  There have been a few attempts at this sort of thing before - Nature tried it once with its "preceedings", but it never took hold. I heard a rumor that this is because a lot of non-science was posted (thinly masked creationism and silly studies about herbal supplement pyramid schemes like Protandim).  So, the bioRxiv has a plan to prevent this:  they've asked a number of people to become "affiliates" whose job it is to screen the preprints to make sure that it is, at least, science.  There will be no judgement about merit, we're to leave that to the communities, but just to screen out non-science.  Anywho, I'll be splitting my pre-print posts between here and the physics arXiv from now on - depending on focus.  More clinical/biological papers will go to the bioRxiv, and more mathematical/methodological will go to the physics arXiv.  For Warburg's Lens, I'll troll both...

I hope you check out the bioRxiv, and, if you are doing work in the biological sciences, I hope you consider posting your work here as you submit to standard journals.  I did a poll recently on a friend's website, and found that the only thing really stopping biologists from posting was...  well...  NOTHING.  Mostly, it was habit and inertia.  So - let's change those.  Let's put our work out there early and often and let the scientific community do its thing!

Tuesday, October 8, 2013

Glioblastoma: Stem cells, plasticity and the niche(s). A summary and introduction to our R-01 submission.

I've had an interest, both clinically and scientifically, in glioblastoma for about 6 years.  This started out because I was given a project as a medical student looking at outcomes of treatment for elderly patients, but has continued and consumed more and more of my conscious and unconscious thought in the intervening years.  For a long time, patients over 70 weren't given the same care as their younger counterparts because it was felt that the treatment was too harsh for them.  This paradigm has begun to change, thanks in some part to the work I was a part of, but the outcomes remain very poor, for all patients.  While I had success in this initial clinical research (first two figs), I was frustrated at what I perceived as a lack of progress, and didn't feel that I was really contributing to this.  This feeling is really what pushed me into basic research...

Unsurprisingly, adding more therapy extends survival in the elderly.  Taken from:
Scott, J. G., Suh, J. H., Elson, P., Barnett, G. H., Vogelbaum, M. A., Peereboom, D. M., et al. (2011). Aggressive treatment is appropriate for glioblastoma multiforme patients 70 years old or older: a retrospective review of 206 cases. Neuro-oncology, 13(4), 428–436. doi:10.1093/neuonc/nor005
Anyways, my story aside, this post is supposed to be about this new research project. So, let me first provide some background. Glioblastoma is the most common primary malignancy of the brain in adults. It carries a poor prognosis of about 1.5-2 years from diagnosis - even with advanced surgery, radiation and chemotherapy.  The nature of this tumor is quite different from all others - it is incredibly invasive, with rogue cells appearing many centimeters from the primary mass.  This is different than most solid tumors, which typically have a sharp edge where the tumor stops and healthy tissue begins.  There may be some small number of cells that slip over, but usually surgeons are able to get a 'clean margin'.  This is not so in glioblastoma - even if the margin appears clean (no cells visible under the microscope), we know from prior experience that there are viable cells at quite a distance.  There is a famous surgical study from the 1930s where doctors removed THE ENTIRE HEMISPHERE of the brain in which these tumors resided, and the patients recurred on the other side (first reported by Dandy, JAMA 1928).

Recursive Partitioning Analysis showing prognostic subgroups for patients over 70.
Taken from: Scott, J. G., Bauchet, L., Fraum, T. J., Nayak, L., Cooper, A. R., Chao, S. T., et al. (2012). Recursive partitioning analysis of prognostic factors for glioblastoma patients aged 70 years or older. Cancer, 118(22), 5595–5600. doi:10.1002/cncr.27570
To combat this, we have tried treating patient's entire brains with radiation (whole brain radiation therapy), but were not able to control these distant recurrences using safe doses, and given every flavor of chemotherapy you can imagine.  Sadly, only one chemotherapy, temozolomide, has been shown to be effective, providing approximately a 6-8 week survival advantage - far from a home run.

Probably the most famous figure in all glioblastoma research - evidence that a chemotherapy significantly improved survival: by about 6 weeks.  Taken from: 
Stupp, R., Mason, W. P., Bent, M. J. V. D., Weller, M., Fisher, B., Taphoorn, M. J. B., et al. (2005). Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. The New England journal of medicine, 352(10), 987–996. doi:10.1056/NEJMoa043330

So, our standard of care is to treat where the tumor was before surgery and a smallish margin around the edges, and hoping that our chemotherapy will take care of the more distant cells.  In 2004, a famous paper from Singh and colleagues identified a small subset of cells within a glioblastoma which seemed to be responsible for these recurrences - and these cells shared many attributes of non-cancer stem cells.  It turned out that these cells were more resistant to radiation - and this gave us hope: maybe we weren't curing these patients because we were targeting the wrong cells!  The field of glioma stem cell biology has advanced rapidly and many scientists are working on the problem.  A prominent group in this field is led by Jeremy Rich at the Cleveland Clinic's Lerner Research Institute.  They have made many advances, but recently their focus has been on the effect of physical/chemical factors within the 'microenvironment' of the tumor that promote these special 'stem' cells - for example acidity, low oxygen tension and low glucose levels.

One of the scientists from this lab in Cleveland, Anita Hjelmeland, recently took a faculty position at the University of Alabama in Birmingham, where they have a massive brain tumor center (called a SPORE) to continue her work.  She and I met when I was visiting her lab in Cleveland and gave a talk about some of the theory work that +David Basanta and I have done.  She and I hit it off, scientifically, and we decided to start a collaboration.  We've worked together now on a few different projects that are in various phases of development, and just yesterday, we submitted an R-01 (a large scale, 5 year grant) proposal that is led by Anita and David, with participation from myself, +Alexander Anderson and +Heiko Enderling.  We are hoping to leverage the strengths of her biological laboratory with our theoretical modeling techniques to try to make some progress against this cancer. Her work previously has shown, convincingly, that hyoxia (low oxygen levels), acidic pH and low glucose levels promote these 'stem' cells, but trying to understand how they all work together is a difficult task - especially in a living system.  This is where our computational models can help.

Anyways, we have our fingers crossed for the success of our grant, and I'll be sure to keep you updated as to our progress.  As a teaser, I am including a figure from our grant.  Mind you, this is unpublished preliminary data (SHARING IN SCIENCE IS GOOD!), so don't draw too many conclusions from it.
Taken from: 
Heddleston, J. M., Li, Z., Mclendon, R. E., Hjelmeland, A. B., & Rich, J. N. (2009). The hypoxic microenvironment maintains glioblastoma stem cells and promotes reprogramming towards a cancer stem cell phenotype. Cell cycle (Georgetown, Tex.), 8(20), 3274–3284.

Some background: it seems that these special 'stem' cells in the tumor preferentially live in special areas called 'niches'. These niches come in (at least) two different varieties, near to the vasculature, where nutrients are abundant, and near to areas of necrosis (cell death) where nutrients are scarce. This difference is intriguing and some observations have suggested that they might contribute to differences in treatment response.  So - the preliminary finding...  our model suggests that the physical microenvironmental history of these niches is very different, and that the evolutionary dynamics within them are as well!  If we can better understand how these niches are created and maintained, maybe we can make some inroads against the progression of this tumor.

Our model, center, has two different areas in which stem cells seem to reside - near to vessels, where the environment is stable, and near to the areas of necrosis, where the environment is harsh. (unpublished data)

So - wish us luck.  The model that we have extended to make the above prediction is under review at PLoS Computational Biology, but you can see a preprint here.  Anita has published a TON of papers on this subject, which you can find on pubmed.  David has also written several papers (a couple with me) on glioblastoma, but only the preprint so far on stem cells in this disease. Our resident stem cell modeling expert, +Heiko Enderling, will be of great help as well.  You can see his long publication record on his website.