Session D42: Focus Session: Physics of Cancer I -- Evolution and Resistance

Drug Resistance and the Kinetics of Metastatic Cancer

Most metastatic cancers after initial response to current drug therapies develop resistance to the treatment. We present cancer data and a theory that explains the observed kinetics of tumor growth in cancer patients and using a stochastic model based on this theory we relate the kinetics of tumor growth to Kaplan-Meyer survival curves. The theory points to the tumor growth rate as the most important parameter determining the outcome of a drug treatment. The overall tumor growth or decay rate is a reflection of the balance between cell division, senescence and apoptosis and we propose that the deviation of the decay rate from exponential is a measure of the emergence of drug resistance. In clinical trials the progression free survival, the overall survival, and the shape of the Kaplan-Meyer plots are determined by the tumor growth rate probability distribution among the patients in the trial. How drug treatments modify this distribution will also be described. At the end of the talk we will discuss the connection between the theory described here and the age related cancer mortality rates in the United States.   

Lattice Boltzmann simulations of lymphatic pumping

Lymphatic flow plays an important role in the progress of many diseases, including lymphedema and metastasis. However lymphatic pumping and flow is poorly understood. Here, we present a computer model that is based on biological observations of lymphatic pumping. Fluid flow is simulated by a D2Q9 lattice Boltzmann model. The boundary of the vessels moves according to shear-induced nitric oxide production, and wall motion transfers momentum to the fluid to induce flow. Because the model only includes local properties, it can be highly parallelized. In our case we utilize graphic processors (GPU) to achieve high performance computation. We show that the model provides stable pumping over a wide range of parameter values, with optimum flow achieved in the biological ranges. Furthermore, we investigate the efficiency by analyzing the flow rate and pumping frequency in order to compare the behavior of the model with existing in vivo data.   

Mechanical and Structural Changes of the Pericellular Coat during Cell Proliferation

The organization of a hyaluronan and proteoglycan-rich pericellular coat at the cell surface has been shown to facilitate cell migration and mitosis. These several microns thick, swollen grafted polymer matrices are directly correlated with efficient proliferation, migration, and in extreme cases have been associated with the metastatic spread of cancer. For example, hyaluronan synthesis is enormously increased when oncogenic viruses transform fibroblasts and elevated levels of hyaluronan are associated with the hyperproliferative and malignant phenotypes in melanoma and various carcinomas. Studies on cancer cell lines have shown that overproduction of hyaluronan and excess proteoglycan enhances their anchorage independent growth, tumorigenicity and metastatic potential. It has long been suspected that the mechanical and structural changes associated with enhanced pericellular matrix are in part responsible for these effects. Here we present measurements of pericellular coat mechanics and structure, investigating how it changes with cell cycle as well as increased or decreased proteoglycan content.   

Can low energy electrons lead to strand breaks in DNA under realistic conditions?

It is widely accepted that low energy electrons produced by ionizing radiation play an important role in causing DNA damage [B. Bouda\"iffa et al., Science {\bf 287}, 1658 (2000)]. Understanding the behaviour of DNA components in the condensed phase due to such electrons is a fundamental step towards modelling this damage within a realistic environment. Here we present a computational study of the effect of low energy electrons in condensed phase models of solvated DNA fragments. First we show that excess electrons, which are initially found delocalized, quickly localize around the nucleobases within a 15 fs time scale. Energies and time scales are comparable for each of the bases [M. Smyth and J. Kohanoff, Phys. Rev. Lett. {\bf 106}, 238108 (2011)]. The phosphodiester bond C$_{3'}$-O$_{3'}$, which under normal conditions is very stable, weakens significantly upon electron attachment both, in the gas and in the condensed phase. Computation of free energy profiles show that barriers for bond cleavage are in the region of 5-8 kcal/mol for all the solvated nucleotides, thus suggesting that this kind of event is quite likely at ambient temperature. This supports the notion that ionizing radiation can actually lead to DNA strand breaks in the physiological environment.   

Emergence of fractal behavior and other changes of cell surface during malignant transformation: AFM study of human cervical epithelial cells

Fractal behavior, self-similarity when zooming in or out, is frequently found in natural patterns emerged from chaos or any far from equilibrium systems. While expected and observed for tissues, the emergence of fractal behavior associated with malignant transformations was not observed at the level of single cell. Here report on the appearance of fractal behavior when normal human cervical epithelial cells become malignant. This was found by analyzing the adhesion maps imaged with AFM working in HarmoniX mode. Normal and malignant (a mix of cancerous and precancerous) cells were enzymatic only extracted from cervical tissue of healthy individuals and cancer patients, respectively. A surprising 100{\%} discrimination of malignant and normal cells was observed. Although we previously reported differences in surface (brush) layer of cancer cells, the unambiguous quantitative divergence of the fractal behavior of the adhesion maps is a surprise (in particular, when compared to no difference found in the regular AFM images). The nature of the observed difference in the adhesion behavior will be discussed. These results may suggest that the fractal dimensionality can be treated as a new potential ``physicomarker'' for detection of individual cervical cancer cells.   

Improved survival in rats with glioma using MRI-guided focused ultrasound and microbubbles to disrupt the blood-brain barrier and deliver Doxil

Blood-brain-barrier (BBB) limits the transportation of most neuropeptides, proteins (enzymes, antibodies), chemotherapeutic agents, and genes that have therapeutic potential for the treatment of brain diseases. Different methods have been used to overcome this limitation, but they are invasive, non-targeted, or require the development of new drugs. We have developed a method that uses MRI-guided focused ultrasound (FUS) combined with circulating microbubbles to temporarily open BBB in and around brain tumors to deliver chemotherapy agents. Here, we tested whether this noninvasive technique could enhance the effectiveness of a chemotherapy agent (Doxil). Using 690 kHz FUS transducer and microbubble (Definity), we induced BBB disruption in intracranially-implanted 9L glioma tumors in rat's brain in three weekly sessions. Animals who received BBB disruption and Doxil had a median survival time of 34.5 days, which was significantly longer than that found in control animals which is 16, 18.5, 21 days who received no treatment, BBB disruption only and Doxil only respectively This work demonstrates that FUS technique has promise in overcoming barriers to drug delivery, which are particularly stark in the brain due to the BBB.   

Insights into protein -- DNA interactions, stability and allosteric communications: A computational study of MutS-DNA recognition complexes

DNA mismatch repair proteins (MMR) maintain genetic stability by recognizing and repairing mismatched bases and insertion/deletion loops mistakenly incorporated during DNA replication, and initiate cellular response to certain types of DNA damage. The most abundant MMR mismatch-binding factor in eukaryotes, MutS, recognizes and initiates the repair of base-base mismatches and small insertion/deletions. We performed molecular dynamics simulations on mismatched and damaged MutS-DNA complexes. A comprehensive DNA binding site analysis of relevant conformations shows that MutS proteins recognize the mismatched and platinum cross-linked DNA substrates in significantly different modes. Distinctive conformational changes associated with MutS binding to mismatched and damaged DNA have been identified and they provide insight into the involvement of MMR proteins in DNA-repair and DNA-damage pathways. Stability and allosteric interactions at the heterodimer interface associated with the mismatch and damage recognition step allow for prediction of key residues in MMR cancer-causing mutations. A rigorous hydrogen bonding analysis for ADP molecules at the ATPase binding sites is also presented. A large number of known MMR cancer causing mutations among the residues were found.   

Glycoprotein Mucin Molecular Brush on Cancer Cells and its Correlation with Resistance Against Drug Delivery

Uptake of cytotoxic drugs by typical tumor cells is limited by the dense dendritic network of oligosaccharide mucin chains that forms a mechanical barrier. Atomic force microscopy is used to directly measure the force needed to pierce the mucin layer to reach the cell surface. Measurements are analyzed by deGennes' steric reputation theory. Multi-drug resistant ovarian tumor cells shows significantly larger penetration load compared to the wide type. A pool of pancreatic, lung, colorectal, and breast cells are also characterized. The chemotherapeutic agent, benzyl-$\alpha $-GalNac, for inhibiting glycosylation is shown to be effective in reducing the mechanical barrier.   

Bcl-2 apoptosis proteins, mitochondrial membrane curvature, and cancer

Critical interactions between Bcl-2 family proteins permeabilize the outer mitochondrial membrane, a common decision point early in the intrinsic apoptotic pathway that irreversibly commits the cell to death. However, a unified picture integrating the essential non-passive role of lipid membranes with the contested dynamics of Bcl-2 regulation remains unresolved. Correlating results between synchrotron x-ray diffraction and microscopy in cell-free assays, we report activation of pro-apoptotic Bax induces strong pure negative Gaussian membrane curvature topologically necessary for pore formation and membrane remodeling events. Strikingly, Bcl-xL suppresses not only Bax-induced pore formation, but also membrane remodeling by disparate systems including cell penetrating, antimicrobial or viral fusion peptides, and bacterial toxin, none of which have BH3 allosteric domains to mediate direct binding. We propose a parallel mode of Bcl-2 pore regulation in which Bax and Bcl-xL induce antagonistic and mutually interacting Gaussian membrane curvatures. The universal nature of curvature-mediated interactions allows synergy with direct binding mechanisms, and potentially accounts for the Bcl-2 family modulation of mitochondrial fission/fusion dynamics.   

Drift, draft, waves, and ratcheting: evolutionary models of cancer progression

Recent evidence has found that many mutations are detrimental to tumor growth in cancer. These mutations, called \textit{passenger mutations,} are distinguished from the better known cancer-causing \textit{driver mutations}, which increase a tumor cell's proliferative capacity. How passenger mutations arise, despite selection against them, is not well understood nor fully explained by existing theory. Here, we extend several population genetics models to explain their accumulation in a precancerous population of cells and compare our findings against stochastic simulations. We find that passenger mutations alter and can avert progression to cancer. The probability of cancer depended heavily, and non-monotonically, on both the deleteriousness and rate of mutations. Counter-intuitively, high mutation rates decrease the likelihood of cancer---a finding recently corroborated by clinical data[1]. Our models suggest that therapies exploiting passenger mutations can avert cancer and may be more effective than targeting driver mutations. \begin{enumerate} \item Birkbak, N.J., et al., \textit{Paradoxical relationship between chromosomal instability and survival outcome in cancer.} Cancer Res, 2011. \textbf{71}(10): p. 3447-52. \end{enumerate}