What drives prostate cancer evolution?

I usually start our papers on prostate cancer to bone metastases by explaining how common prostate cancer is and how little can we do for a patient when the disease metastasizes. But the good news is that only about 1 in 10 patients die of prostate cancer. One of the questions when dealing with a new prostate cancer patient is not how to treat the cancer but whether treatment should be given.

To make this decision, pathologists look at tissue sections (see the featured image) and decide, based on the size and shape of the cancer cells and whether tissue architecture seems to be destroyed. With that information (and two representative examples) they produce a Gleason score with values ranging from 2 (no tumor) to 10 (most aggressive one). One thing that is generally overlooked is the prostate ecosystem. Prostate cancer cells emerge from epithelial cells whose work is supported by smooth muscle cells, fibroblasts and others. These stromal cells can produce an environment that is permisive to the tumor (in the case of reactive stroma). Why haven’t we used information about stroma before? This week we have released a bioRxiv preprint that shows how this can be done. This manuscript constitutes a substantial body of work including a sophisticated computational model (Sandy Anderson, Ziv Frankenstein and yours truly) to explore our hypothesis that led to a clinical biomarker tested on historical clinical data (Gustavo Ayala) and in vivo validation (Simon Hayward, Omar Franco and Doug Strand).

Using a computational model we can explore how the interactions between a heterogeneous cancer population (more or less aggressive cancer cells) and an also heterogeneous stroma (more or less permissive stromal cells) can lead to vastly different evolutionary paths and thus, clinical outcomes. Here’s an example where we look at the tumor growing, starting from one of the glands and gradually taking over the prostate:

We can also see the tumor phenotypes leading the charge:

Using this model we learned the impact that a permissive stroma has on the evolutionary dynamics of prostate cancer.

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The more help we get, the less we need to change
Highlighting the importance of computationally driven approaches (which can study vastly more scenarios more efficiently and cheaply than any experimental model) is the fact that this dialogue can lead to rather counterintuitive outcomes. For instance that less permissive microenvironments (with more reactive stroma) can, paradoxically, select for tumor cells that are (relatively) less aggressive.
With these insights in mind, we propose an Integrated Cancer Biomarker (ICB) which we tested using a cohort of historical data from 870 patients.
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Patient stratification of Gleason categories using the ICB

Clearly , integrating pathological information from both the tumor and the stroma allows us to better predict how the tumor will turn to be from the clinical perspective. Adding further credence to the results is that we decided to validate the biological mechanism we used to build the computational model with an animal model.

I am excited about this paper because it shows what a mathematical model can do when mathematicians, biologists and clinical researchers work together. If you want to know the details, check out the bioRxiv version here.

Dr. Jake Taylor-King

Congratulations to Jake who has just passed his viva and, pending minor revisions, will receive a DPhil in mathematics for the work he developed while working under the supervision of Prof. Jon Chapman at Oxford’s Mathematical Institute, Mason Porter at UCLA and yours truly here at Moffitt.

During his doctoral studies Jake worked with collaborators of this group like Conor Lynch and Andriy Marusyk to understand cancer biology through network modeling. Together with Conor, Jake developed a model of osteocyte growth which allows us to understand how tumor cells can disrupt this process and lead to pathological bone. Together with Andriy, Jake developed a technique he named simulated ablation to study the signaling impact of cells to other cells in their environment.

Along the way Jake was awarded the Lee Segel prize for his previous work on velocity jump processes.

So congratulations Jake, we are eager to see what will you revolutionize next!

Welcome Niccolò Totis

Niccolò is a trained physician that realized that there are more ways to contribute to medicine other than seeing patients. As a result, he started a PhD at the University of Turin, Italy, working with Marco Beccuti, Francesca Cordero and Gianfranco Balbo, developing mathematical models of tumor metabolism.

After coming to Tampa last November to attend the 5th IMO Workshop, he decided that it would pay to spend more time here. So for the next half year Niccolò and us will be working together on an agent-based model of metabolic heterogeneity in cancer. Stay tuned.

Dark selection in CMML

One more year one more IMO Workshop. This year our group worked on CMML or Chronic MyeloMonocytic Leukemia, a relatively rare blood cancer. As usual in IMO workshops our team included clinical (physician and malignant hematology specialist Eric Padron), cancer biologists (Andriy Marusyk and Daria Miroshnychenko) and mathematical modelers from Moffitt, Cleveland Clinic, Oxford, Yale and Harvard. A crack team of interdisciplinary researchers that I was lucky to be part of.

The JAK pathway is considered a driver of CMML and fortunately a drug known as ruxolitinibruxolitinib can target cells whose growth is driven by JAK. Unfortunately, as it is the case with most targeted treatments, ruxolitinib quickly leads to the emergence of resistance and relapse. While this is not entirely surprising, the interesting bit is that neither allele frequency nor tumor burden are impacted by the treatment. What exactly drives ruxolitinib resistance?

Team member Artem Kaznatcheev has written about the basis of our project before so please start by taking a look there. Our group produced a suite of models where we consider three distinct possibilities: that there is a subtle Darwinian selection force impacting proliferation rates, that a (provocatively named) Lamarckian force is driving resistance or that non cell-autonomous mechanisms are in place. We clearly thought of something that resonated with the workshop judges as we were awarded a pilot grant to test this experimentally so stay tuned.

Postcard from Bielefeld: modeling selection in cancer evolution

I am currently in a small  city in Germany: Bielefeld, as a guest of the Center for Interdisciplinary Research (ZiF in German) of the University of Bielefeld. During this time I will be working with other ZiF fellows on a couple of projects which I hope to discuss some other time. This work will be within the framework of a ZiF cooperation group called Multiscale Modeling of Tumor Initiation, Growth and Progression.

To kick start this,  the organizers of this cooperation group have also organized a small workshop on mathematical modelling of cancer evolution. This being exactly the topic of my research for the last decade meant I was really excited to participate. The image at the top of this post shows many (but not all) of the participants.

Any interdisciplinary meeting will include people from at least two disciplines with the goal of the meeting being to establish some sort of bridge between them. In this case I could argue that the disciplines were mathematicians working on less applied topics  vs those working on more applied ones (or biologists as one of them referred to us).

But where I stand, the more interesting gap to bridge was between those interested on the genetic aspects of cancer evolution and those (me and Indiana’s James Glazier) which focused instead on the role of selection. If you ask me (and by reading these lines you have implicitly done so) both genetic variation and selection are the two pillars of evolution and should be considered equally important. Nonetheless there seems to be a lot more work done in trying to understand genetic mutations and phylogenetic trees than in trying to see how the microenvironment and interactions between different cells determines which phenotypes will succeed and which ones will not. More importantly, selection is a key aspect of evolution that we need to understand if we want to have any success when applying treatments to anything from cancer to bacteria to viruses. Why are they (apparently) vastly more people working on genetic aspects rather than selection?

workflow

I think that this difference between workflows might partly explain why. There is a wealth of biological data, much of which is genetic in nature, which requires a comparatively modest degree of collaboration with experimentalists if you are a modeler. The process is described in the previous figure: use a mathematical model to find out what the data tells you and then generate hypotheses out of it.

Working on selection requires a different approach as there’s not much data available, especially data that could be easily slotted in a mechanistic model of cancer evolution. Here the mathematical model, built after much consultation with domain experts (that is, cancer biologists) is built to explore the biology and yield hypotheses, which, since we involved our experimental partners from the start, will be also explored in vivo or in vitro. This route is harder but also relatively unexplored, want to join?

 

Again: come join us!

A couple of months ago we got news that the NCI has awarded us a U01 grant to continue our work defining the bone ecosystem and how prostate cancer can come in and disrupt it. Of course this is something that cannot be done in a hurry so we are in this for the long-haul. We also need help. We have Conor Lynch and his lab as the willing partners for this work but we also need you.

And who are you, you might be (weirdly) asking yourself ? A lot of what we need was described in this post. Shall I start with a PhD in physics/maths/CS? the need to be able to think mathematically and (hopefully) be able to develop in a programming language like C++/Java/Python or others of the sort?  Those are a must but  not the most important quality to work in a place like ours.

Basically we want you to be a detective of cancer biology, able to work with other people, happy to discuss your ideas with either mathematicians, biologists and oncologists. Gregarious but also independent you want to try new ways to think about cancer treatment

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That this sound like you? Then email me and also look for job #20125 at https://moffitt.org/careers-education/