Physics and Cancer II Workshop

Physics and Cancer II: Theoretical Foundations of Drug and Immune Resistance in Cancer

A workshop held in Arlington, VA on November 13-14, 2012

Physics and Cancer II:  Theoretical Foundations of Drug and Immune Resistance in Cancer

A workshop held in Arlington, VA on November 13-14, 2012

Physics & Cancer II: Arlington VA November 14, 2012

Physics and Cancer II Workshop Attendees.  L-R:  Jerry Lee, NCI/NIH; Patrick Dennis, Janelia/HHMI; Nas Kuhn, NCI/NIH; Sui Huang, ISB; Clark Cooper, NSF; Larry Norton, Sloan-Kettering; Eytan Domany, Weizmann Inst; James Smith, LANL; Gyan Bhanot, Rutgers; David Tarin, UCSD; Bob Laughlin, Stanford; Eric Holland, Sloan-Kettering; Reka Albert, Penn State; Walt Stadler, U of Chicago; Chris Smith, Rice U.;  Eshel Ben-Jacob, Tel Aviv U.;  Wilfred Stein, Hebrew U./NCI;  Donald Coffey, JHU; Krastan Blagoev, NSF; Herb Levine, Rice U.; Jonathan Franca-Koh, NCI/NIH; Donna Hansel, CCF; Jose Onuchic, Rice U.; Jessie Au, Ohio St U.; Nicole Moore, NCI/NIH; Bruce Rosen, Harvard; Tito Fojo, NCI/NIH; Susan Bates, NCI/NIH; Darryl Shibata, UCSD; Thomas Flaig, UCO; Ivan Matic, INSERM.   Not pictured: Denise Caldwell, NIH; Curt Callan, Princeton; Wafik El-Deiry, Penn St; Michael Espey, NCI/NIH; Larry Nagahara, NCI/NIH; Kieth Orford, GlaxoSmithKline; Kamal Shukla, NSF; James Yang, NCI/NIH

Physics and Cancer II was a two-day workshop addressing the “Theoretical Foundations of Drug and Immune Resistance in Cancer” will be held in Arlington, VA on November 13 and 14, 2012. Resistance to treatment is a main reason for cancer deaths and is becoming increasingly relevant in the light of new therapies based on specific molecular targets and/or specific priming of the immune response. This resistance can involve genetic changes (most likely selection of more resistant clones from an existing multi-clonal population), epigenetic changes (modifying gene expression as a way of bypassing the drug action, possibly changing splicing patterns as has been seen recently in melanoma), and tissue-level heterogeneity (the creation of pockets within the tumor which prevent access). Unraveling the interplay of these different mechanisms so as to create a quantitative approach to both understanding and most important defeating these adaptive processes is a very high priority.

The goal of the workshop is to bring the theoretical physics community and the oncology research community to discuss the state of our knowledge of drug and immune resistance in cancer. We expect to invite roughly 15 physicists and a matching number of oncologists. The workshop will be two full days and will feature an extremely limited number of talks followed by long discussions and brainstorming sessions.

AGENDA

BIOS

The Need for Physics Style Theories of Cancer

While reading Bob Weinberg’s cancer textbook, it’s striking that this beautifully written book lacks any mathematical formulas. Can we really understand and cure cancer without developing quantitative theories that relate different observations to each other? If the answer is yes, then how do we know that our understanding of one aspect of cancer is logically consistent with other aspects of the disease. For example, how can we be sure that the scenarios described in textbooks on cancer development through successive mutations and clonal expansions, the mechanisms of DNA damage and repair, the kinetics of cell division in tissue, etc. are not in logical contradiction with each other. These questions are also true with regard to biology as a whole, but some parts of biology have become very quantitative (and successful), so we will focus on cancer. Mathematics is the only tool known of that comes close to a guarantee that our theories are logically consistent.

Cancer is a complicated disease that develops in space and time. It engulfs all aspects of biology, from development to aging, from single cellular organisms to complicated multi-cellular organisms. It is likely that there are multiple routes to cancer. As such, it has common characteristics with complex systems that we encounter in physics, like high temperature superconductors, liquid crystals, sand, systems with several competing order parameters, and stochastic nonlinear dynamical systems to name a few. Approaching these phenomena has not been easy, but we have made substantial progress and there is no reason to believe that the same approach cannot be helpful in cancer.

The physics community interested in cancer needs to know what has been established in cancer with certainty, what are the important observations that give insights into further questions and what are anecdotal stories, which although entertaining are distractions on the way to the real important facts. I believe that to be able to distinguish between the important and unimportant we will need to discover mathematical relationships between different observable parameters, devise and perform experiments to check their validity, and establish when these relationships break. We will need to ask the BIG questions of universality and build theoretical foundations at each significant spatial and temporal scale. Our goal is to have a predictive understanding of cancer initiation and progression, which will help us to devise treatment strategies.

We hope that this website and our effort to bring theory to cancer will play a vital role in our understanding and cure of this devastating disease.

The Physics and Cancer Website Organizers

Eshel Ben-Jacob, Tel Aviv University

Krastan B. Blagoev, National Science Foundation

Herbert Levine, Rice University

While reading Bob Weinberg’s cancer textbook, it’s striking that this beautifully written book lacks any mathematical formulas. Can we really understand and cure cancer without developing quantitative theories that relate different observations to each other? If the answer is yes, then how do we know that our understanding of one aspect of cancer is logically consistent with other aspects of the disease. For example, how can we be sure that the scenarios described in textbooks on cancer development through successive mutations and clonal expansions, the mechanisms of DNA damage and repair, the kinetics of cell division in tissue, etc. are not in logical contradiction with each other. These questions are also true with regard to biology as a whole, but some parts of biology have become very quantitative (and successful), so we will focus on cancer. Mathematics is the only tool known of that comes close to a guarantee that our theories are logically consistent.

Cancer is a complicated disease that develops in space and time. It engulfs all aspects of biology, from development to aging, from single cellular organisms to complicated multi-cellular organisms. It is likely that there are multiple routes to cancer. As such, it has common characteristics with complex systems that we encounter in physics, like high temperature superconductors, liquid crystals, sand, systems with several competing order parameters, and stochastic nonlinear dynamical systems to name a few. Approaching these phenomena has not been easy, but we have made substantial progress and there is no reason to believe that the same approach cannot be helpful in cancer.

The physics community interested in cancer needs to know what has been established in cancer with certainty, what are the important observations that give insights into further questions and what are anecdotal stories, which although entertaining are distractions on the way to the real important facts. I believe that to be able to distinguish between the important and unimportant we will need to discover mathematical relationships between different observable parameters, devise and perform experiments to check their validity, and establish when these relationships break. We will need to ask the BIG questions of universality and build theoretical foundations at each significant spatial and temporal scale. Our goal is to have a predictive understanding of cancer initiation and progression, which will help us to devise treatment strategies.

We hope that this website and our effort to bring theory to cancer will play a vital role in our understanding and cure of this devastating disease.

The Physics and Cancer Website Organizers

Eshel Ben-Jacob, Tel Aviv University

Krastan B. Blagoev, National Science Foundation

Herbert Levine, Rice University

Creating the Field of the “Physics of Cancer”

A recent review paper on metastatic spread brings to the fore one of the most important questions that needs to be addressed in the creation of a physics of cancer. The basic issue is, why do the cells in the primary tumor develop the genetic and epigenetic properties that enable them to migrate through the body and establish successful (from the tumor’s perspective) metastatic outposts.


A recent review paper on metastatic spread brings to the fore one of the most important questions that needs to be addressed in the creation of a physics of cancer. The basic issue is, why do the cells in the primary tumor develop the genetic and epigenetic properties that enable them to migrate through the body and establish successful (from the tumor’s perspective) metastatic outposts. It is hard to believe that these properties are selected for by direct evolutionary pressure, as the probability of success is extremely small and cells acting independently would have a huge advantage if they just stayed put. An answer to this puzzle could inform treatments that deter metastatic spread, which after all is the cause of death in a vast majority of cases.

Before proceeding to possible resolutions, it is important to point out that metastatic growth seems to be difficult even for cells that have already done it once. One can take cells from a metastasis and implant them into fresh tissue (in a mouse model, of course) and determine the rate of successful colonization. One can then repeat the process several times to enrich for growth potential. It seems that even these cells can form secondary tumors with low probability (perhaps 1%). So, whatever the final bottleneck is in metastatic inefficiency, it does not appear that one can totally eliminate it by direct selection.

The simplest proposition to explain these observations would be to combine random genetic variation with the need for a minimum size of nucleation for tumors. The idea here is that as the primary tumor becomes more and more genetically unstable, clones emerge that are motile and that have a much reduced nucleation barrier. Exactly how long this would take to occur is impossible to estimate given our ignorance regarding the mapping from genotype to phenotype. This scenario could explain examples where cells leave the primary tumor quite early on (it is undoubtedly easier to turn on motility) but fail to establish metastases until much later. This delay could just be a numbers game (as the primary tumor grows, more cells are released increasing the cumulative odds) but surmounting an exponential barrier is usually accomplished by lowering the barrier, not increasing the prefactor. This concept does not explain why the barrier cannot become zero for the proper clone. It may be that colonization happens occurs before that (due to the large prefactor) and hence the cells never get a chance to become fully capable or it may be that a majority of the cells switch out of the capable state once growth begins; this is similar to differentiation of normal stem cells, and only the residual “cancer stem cells” are sill colonization-capable. This could be tested by attempt to enhance the percentage via selection based on stem-cell markers.

A different conceptual approach is taken by Norton and co-workers, with related work by Carlos Maley. In their formulation, cells are selected for migratory properties so as to help the primary tumor grow more efficiently. This motility may allow both for local motion and for what has been called self-seeding, namely that cells actually leave the tumor, circulate through the blood and lymph systems, and return back to the same tumor. Some evidence for this has been presented, again of course in a mouse model. It seems to me that this approach may help explain the motility transition but does nit really address why these cells can colonize foreign tissues; this again appears to be left to chance genetic changes of these now motile cells, changes that presumably are not needed to reattach to the primary tumor. This could all be investigated experimentally, bu has not yet been done so.

A last speculative idea returns to the notion of differentiation, but now within the context of the primary tumor. There are many cases in biology in which intercellular signaling maintains a small subpopulation of cells in a state which makes no sense from a purely individualistic perspective. One well-=known example is that of the persister phenotype in E. Coli, which have greatly diminished growth so as to provide an advantage to the colony as a whole. Tumors might create a reservoir of seeding cells (with both migratory and colonization capabilities) as insurance against environmental disaster; these cells would have some characteristics of stem cells, but need not be a fixed subpopulation. This idea meshes with the previous explanation for why the typical cells in a metastasis are  not very colonization-capable, but many, many questions remain. The role of genetic versus epigenetic degrees of freedom is obscure; cancer cells seem to make much more use of genetic variation than do, for example, bacterial colonies. It is less obvious how to explain “metastatic tropism” (the strong correlation between primary tumor site and metastasis location); in the nucleation picture, one can easily imagine a barrier that varies with target tissue type. Perhaps even the maintained seeding cells are not equally well-matched to alternate sites for spread, and probably even these cells have some sort of growth barrier to surmount.

It is our job as physicists to connect these conceptual pictures with doable experimental tests. It is only then that we can truly be on the road to creating the field of the “physics of cancer”.

Societal interactions in ovarian cancer metastasis: a quorum-sensing hypothesis.

Clin Exp Metastasis. 2009;26(1):67-76. Epub 2008 May 31.

Source

The Department of Obstetrics and Gynecology, The University of Chicago, Chicago, IL 60637, USA.

Abstract

The biochemical and biological mechanisms metastatic cancer cells use to function as communities and thwart internal and external growth control mechanisms remain undefined. In this work, we present the hypothesis that cancer cells may use a Quorum-Sensing mechanism to regulate multicellular functions and control steps in metastatic colonization. Quorum sensing is a bacterial cell-cell communication process used to track increasing cell-population density and, in response to changes in cell number, coordinate gene expression and behavior on a community-wide scale. Important parallels between the behavior of societies of bacterial cells and societies of malignant cancer cells exist in the bacterial literature. Of relevance to metastasis is the finding that pathogenic bacteria use quorum sensing to determine when their population numbers are high enough to collectively form biofilms in or on host organisms. Biofilms are complex, heterogeneous communities of bacterial cells encased within an extracellular matrix attached to a solid surface. Biofilms exacerbate disease and are refractory to a battery of therapies. We suggest that thequorum-sensing-controlled bacterial biofilm formation process closely parallels the steps in metastatic colonization. Cells migrate toward/on target surfaces (organ-specific homing), show cell-cell and cell-matrix interactions (tumor cell-stromal cell crosstalk), remain subclinical until they can mount an effective attack (dormancy), form complex structures with channels for nutrient flow (vascularized lesions), and contain resistant cells which can cause disease recurrence (persistors). Using ovarian cancer as an example, we present data supporting the connection between metastatic colonization and quorum sensing and discuss the implications for understanding and controlling metastasis formation.

PMID: 18516689
 [PubMed – indexed for MEDLINE]

Link to Full Article

The Physics of Cancer – Food for Thought

The Physics of Living Systems Community has collectively become excited at the possibility of contributing to a better understanding of cancer. The signs of this are manifold. There is a workshop scheduled next spring at the KITP in Santa Barbara on the Physics and Mathematics of Cancer, co-organized by physicists and by cancer biologists. There is a tutorial on Sunday at the upcoming American Physical Society March meeting in Boston to introduce this subject to interested attendees. There is a special issue of the journal Physical Biology (Vol 8.,No. 1 in 2011) devoted to research at the National Cancer Institute sponsored Physical Science Oncology Centers. And, we here at the Center for Theoretical Biological Physics will be starting a new synergy research area devoted to this topic.

The Physics of Living Systems Community has collectively become excited at the possibility of contributing to a better understanding of cancer. The signs of this are manifold. There is a workshop scheduled next spring at the KITP in Santa Barbara on the Physics and Mathematics of Cancer, co-organized by physicists and by cancer biologists. There is a tutorial on Sunday at the upcoming American Physical Society March meeting in Boston to introduce this subject to interested attendees. There is a special issue of the journal Physical Biology (Vol 8.,No. 1 in 2011) devoted to research at the National Cancer Institute sponsored Physical Science Oncology Centers. And, we here at the Center for Theoretical Biological Physics will be starting a new synergy research area devoted to this topic.

So, what gives? I think the answer here lies in the fact that physical science can offer both tools and concepts that could help deal with the amazing complex story of cancer as it has become to be understood. Aside from some special cases, attempting to cure cancer by following the simple path of finding a single defect (perhaps one key mutation leading to constitutive activity of a signaling protein) and then devising a small molecule therapy just has not proven to be a powerful enough strategy. In fact, cancers often respond to such treatment with short-term retraction followed inexorably by long-term renewed vigor. This defeat of therapy can occur by a variety of individual cell changes (resistance mutations for example), by collective changes within the entire tumor, by recruitment of surrounding normal cells; the details are sorely absent. Surely coupled to this is the fact that cancers are remarkably heterogeneous in their genomic profiles and in their physical manifestations; there are many redundant pathways leading to similar dire consequences. We as a society are thus faced with the prospect of pending hundreds of thousands of dollars per patient on drugs that increase life expectancy by merely a few months. It may be the height of hubris to think that physicists can make progress on topics that have resisted the best efforts of the oncology community, but there is certainly a strong motivation to try.

And, there are good intellectual reasons as well to work on cancer. Cancer touches on some of the most basic questions underlying biology, related to the plasticity of genetic degrees of freedom, the nature of cell differentiation, the constraints that multi-cellularity places on the proliferation and selfish behavior of individual cells, the role of environment in both genotypic selection and phenotypic behavior etc. There is room here for working on evolutionary dynamics, on genetic systems that control cell fate, on the mechanics of cell motility, on high-resolution imaging inside the human body, and on the design of drug delivery systems. So, as you ponder where you can make your own personal contributions to the Physics of Living Systems, do not overlook the possibility of working on the physics of cancer; it is one of the true challenges of our time.

Prof Herbert Levine, Rice University

Key Questions asked by Cancer Researchers at 11/10 Physics of Cancer Metastasis Workshop

A list of physics and cancer research challenges compiled by Lalit Patel at the University of Michigan from the attendees of the NSF Physics of Cancer Metastasis seminar held in Arlington, VA in November 2010.

A list of physics and cancer research challenges compiled by Lalit Patel at the University of Michigan from the attendees of the NSF Physics of Cancer Metastasis workshop held in Arlington, VA in November 2010.

The Physics of Cancer Metastasis meeting brought together scientists in both the physical sciences as well as the biological sciences with the intent of spawning an interdisciplinary dialogue regarding the unresolved questions in metastatic tumor biology. The conference agenda ended with an open discussion in which attendees were asked to identify two-to-three “Holy Grails” –  questions that if tackled in an interdisciplinary manner could lead to fundamental advances in our understanding of metastatic cancer. The ideas discussed were diverse but fell into distinct categories.

Modeling Disease
The following ideas and challenges were mentioned with respect to quantitative modeling:
  • Using population genetics and evolutionary game theory to parameterize patterns of progression
  • Models that predict the minimum number of mutations and the temporal order of mutations that confer a metastatic vs local phenotype
  • Developing readouts for mathematical models that can be validated using clinical observation
  • Modeling requires a sense of scale. Molecular events happen on a very different space and time scale than cell trafficking or tissue microstructure changes.
  • Quantitative models of tissue patterning that is inclusive of physical and biological factors
  •  The following ideas were mentioned with respect to experimental models:
  • T and B cells undergo genetic translocation, have memory behavior, demonstrate tissue invasiveness, are bone and lymph homing, and do not demonstrate anoikis. The biology of lymphocytes may be a model for metastatic processes in cancer
  • Identifying the simplest creature that develops cancer may help get past the complexity of human tumors and allow investigation into the essentials/fundamentals of cancer
Observing Disease
The group’s interest in direct observation of clinical disease was motivated as much by discussions of metastasis biology as by a desire to obtain data needed to validate quantitative models. In some cases specific technological advances were suggested. In other cases the type of observational data desired was identified while leaving the modality of observation open. The specific ideas mentioned were:
  • Quantitative observation of cells entering circulation at primary tumor site and leaving at metastatic site for temporal analysis, validation of quantitative models, and hypothesis formation regarding mechanisms of dissemination and invasion
  • Using liquid biopsies and temporal analysis for probability distributions for where, in which patients, and over what period of time cells disseminate to different sites
  • Developing imaging techniques distinguishing “hot” tumors from boring ones
  • In vivo metabolic rates
  • Coupling tissue structure observation with pattern recognition for prediction
  • Cytometry in situ of primary tumor, blood, and secondary tissues to observe cells leave, which ones stay in the blood, and which invaded
  • Sensors for where cells move through the body to enable temporal observational studies
  • Imaging technology that permits microstructure observation perhaps
  • Using secondary harmonics and magnetic spectroscopy to observe tissue-scale interactions with disseminated cancer
  • Imaging technology that is sensitive enough to image rare cells like CTCs and DTCs
  • Some genetic anomalies are more interesting than others – how do we observe the emergence of these anomalies in situ?
  • Observation of dormant micrometasases to get at the question of whether it is mass dormancy (death rate = birth rate) or if it is cellular dormancy (birth rate = 0 and death rate = 0)
  • Clinical observation of difference in epigenetic/gentetic state of primary vs metastatic tumors and its association with difference in proliferation rate between primary vs metastatic tumors
  • We know its faster, but how much faster?
  • What is the genetic basis of faster?
  • Is the driver of changes in proliferative behavior genetic or epigenetic?
  • Include observations of tissue structure difference to see if it could be the microenvironment
  • In vivo sensors of tissue structure and forces
The Physical Biology of Disease
Some of the most creative ideas discussed centered on the applications of mechanobiology to metastasis. There was also discussion on the application of thermodynamics to understanding metastatic cancer cell biology. In both spaces there were more questions than answers. They include:
  • What is the role of cell and tissue scale forces in cancer cell’s spreading, seeding, and remodeling  secondary sites
  • Is cancer pushed out of the primary tumor site? Does it crawl out? Is it passively let out? How can we target the processes associated with each of these models of cancer-cell-ejection to minimize metastatic spread?
  • What physical attributes distinguish cells that stay in the primary site versus cells that leave? Is it “stickiness”? If so can we keep them from unsticking? Or is it motility and can we reduce their motility?
  • “Capture Therapy”
  • Assuming that its stickiness can we trap cancer cells from circulation by making a specifically sticky fake secondary environment to prevent them from seeding new tumors?
  • If so what physical and chemical attributes would make for a good trap?
  • Will require biology, quantitiative modeling, and clinical observation to accomplish this goal
  • Thermodynamics of disease
  • What energy utilization efficiency differences exist between “hot” vs “boring” cancer?
  • Can we formalize the Warburg effect?
  • Metabolism differences are already used for imaging, but is there something about energy utilization that can be targeted for treatment?
  • How does cancer affect the mechnobiology and microstructure of the tissue it resides in?
  • Changes in vessel (vascular and lymphatic) permeability
  • Interstitial pressure changes
  • Changes in transport processes defining gradients and patterns of chemotaxis?
  • Biological and clinical consequences of these changes?
  • Can we build a bridge between the mechanobiology and the molecular biology of disease?
  • The biologists framed their ideas in genetic and epigenetic terms.
  • The physicists discussed forces-transduction, tissue structure, cell shape, motility
  • Ingber’s talk demonstrated the beginnings of a bridge between the two with evidence of gene-expression attractor states being adopted in response to mechanical stimuli
  • Can we complete this bridge by delineating how cells translate mechanical stimuli lead into changes in molecular phenotype?