Establishment and characterisation of testicular cancer patient-derived xenograft models for preclinical evaluation of novel therapeutic strategies.

Testicular cancer (TC) is the most common solid tumour in young men. While cisplatin-based chemotherapy is highly effective in TC patients, chemoresistance still accounts for 10% of disease-related deaths. Pre-clinical models that faithfully reflect patient tumours are needed to assist in target discovery and drug development. Tumour pieces from eight TC patients were subcutaneously implanted in NOD scid gamma (NSG) mice. Three patient-derived xenograft (PDX) models of TC, including one chemoresistant model, were established containing yolk sac tumour and teratoma components. PDX models and corresponding patient tumours were characterised by H&E, Ki-67 and cyclophilin A immunohistochemistry, showing retention of histological subtypes over several passages. Whole-exome sequencing, copy number variation analysis and RNA-sequencing was performed on these TP53 wild type PDX tumours to assess the effects of passaging, showing high concordance of molecular features between passages. Cisplatin sensitivity of PDX models corresponded with patients' response to cisplatin-based chemotherapy. MDM2 and mTORC1/2 targeted drugs showed efficacy in the cisplatin sensitive PDX models. In conclusion, we describe three PDX models faithfully reflecting chemosensitivity of TC patients. These models can be used for mechanistic studies and pre-clinical validation of novel therapeutic strategies in testicular cancer.

Testicular cancer: Determinants of cisplatin sensitivity and novel therapeutic opportunities.

Testicular cancer (TC) is the most common solid tumor among men aged between 15 and 40 years. TCs are highly aneuploid and the 12p isochromosome is the most frequent chromosomal abnormality. The mutation rate is of TC is low, with recurrent mutations in KIT and KRAS observed only at low frequency in seminomas. Overall cure rates are high, even in a metastatic setting, resulting from excellent cisplatin sensitivity of TCs. Factors contributing to the observed cisplatin sensitivity include defective DNA damage repair and a hypersensitive apoptotic response to DNA damage. Nonetheless, around 10-20% of TC patients with metastatic disease cannot be cured by cisplatin-based chemotherapy. Resistance mechanisms include downregulation of OCT4 and failure to induce PUMA and NOXA, elevated levels of MDM2, and hyperactivity of the PI3K/AKT/mTOR pathway. Several pre-clinical approaches have proven successful in overcoming cisplatin resistance, including specific targeting of PARP, MDM2 or AKT/mTOR combined with cisplatin. Finally, patient-derived xenograft models hold potential for mechanistic studies and pre-clinical validation of novel therapeutic strategies in TC. While clinical trials investigating targeted drugs have been disappointing, pre-clinical successes with chemotherapy and targeted drug combinations fuel the need for further investigation in clinical setting.

Dual mTORC1/2 Inhibition Sensitizes Testicular Cancer Models to Cisplatin Treatment.

Testicular cancer is the most common cancer type among young men. Despite highly effective cisplatin-based chemotherapy, around 20% of patients with metastatic disease will still die from the disease. The aim of this study was to explore the use of kinase inhibitors to sensitize testicular cancer cells to cisplatin treatment. Activation of kinases, including receptor tyrosine kinases and downstream substrates, was studied in five cisplatin-sensitive or -resistant testicular cancer cell lines using phospho-kinase arrays and Western blotting. The phospho-kinase array showed AKT and S6 to be among the top phosphorylated proteins in testicular cancer cells, which are part of the PI3K/AKT/mTORC pathway. Inhibitors of most active kinases in the PI3K/AKT/mTORC pathway were tested using apoptosis assays and survival assays. Two mTORC1/2 inhibitors, AZD8055 and MLN0128, strongly enhanced cisplatin-induced apoptosis in all tested testicular cancer cell lines. Inhibition of mTORC1/2 blocked phosphorylation of the mTORC downstream proteins S6 and 4E-BP1. Combined treatment with AZD8055 and cisplatin led to reduced clonogenic survival of testicular cancer cells. Two testicular cancer patient-derived xenografts (PDX), either from a chemosensitive or -resistant patient, were treated with cisplatin in the absence or presence of kinase inhibitor. Combined AZD8055 and cisplatin treatment resulted in effective mTORC1/2 inhibition, increased caspase-3 activity, and enhanced tumor growth inhibition. In conclusion, we identified mTORC1/2 inhibition as an effective strategy to sensitize testicular cancer cell lines and PDX models to cisplatin treatment. Our results warrant further investigation of this combination therapy in the treatment of patients with testicular cancer with high-risk relapsed or refractory disease.

A Mathematical Model for the Effect of Low-Dose Radiation on the G2/M Transition.

We develop a mathematical model to study the immediate effect of low-dose radiation on the G2 checkpoint and the G2/M transition of the cell cycle via a radiation pathway (the ATM-Chk2 pathway) of an individual mammalian cell. The model consists of a system of nonlinear differential equations describing the dynamics of a network of regulatory proteins that play key roles in the G2/M transition, cell cycle oscillations, and the radiation pathway. We simulate the application of a single pulse of low-dose radiation at different intensities ([Formula: see text] 0-0.4 Gy) and times during the latter part of the G2-phase. We use bifurcation analysis to characterize the effect of radiation on the G2/M transition via the ATM-Chk2 pathway. We show that radiation between 0.1 and 0.3 Gy can delay the G2/M transition, and radiation higher than 0.3 Gy can fully activate the G2 checkpoint. Also, our results show that radiation can be low enough to neither delay the G2/M transition nor activate the G2 checkpoint ([Formula: see text] 0.1 Gy). Our model supports the idea that the cell response to radiation during G2-phase explains hyper-radiosensitivity and increased radioresistance (HRS/IRR) observed at low dose.

Evidence of intraspecific prey switching: stage-structured predation of polar bears on ringed seals.

Prey switching is a phenomenon in which a predator disproportionately consumes the most abundant prey type, and switches to preferentially consume another prey type if the first becomes relatively rare. This concept may be expanded outside of its usual usage describing switching between prey species (interspecific), to describe switching between prey stages within a given species (intraspecific). Polar bears (Ursus maritimus) are thought to seek out naive ringed seal (Pusa hispida) pups in the spring, but how that may change in years with low seal productivity is unknown. We addressed two main questions: If polar bears typically select for ringed seals' pups, how does this change in years with reduced ringed-seal productivity? How does polar bear predation during years with low ringed-seal productivity impact the ringed seal population? We created a matrix population model for ringed seals to get an estimate of each stage's availability to polar bears in the spring. These estimates of availability were combined with existing studies on the ages of seals consumed by polar bears in years of both high and low ringed seal productivity. Our results suggest that polar bears typically strongly select for ringed seal pups, but switch to disproportionately select older ringed seals in years with low pup availability. The effects of this on ringed seal population growth appear negligible. Non-intuitive results on the effect of prey switching on the prey population emphasize the importance of considering environmental sequences rather than individual years.

Direction-dependent interaction rules enrich pattern formation in an individual-based model of collective behavior.

Direction-dependent interaction rules are incorporated into a one-dimensional discrete-time stochastic individual-based model (IBM) of collective behavior to compare pattern formation with an existing partial differential equation (PDE) model. The IBM is formulated in terms of three social interaction forces: repulsion, alignment, and attraction, and includes information regarding conspecifics' direction of travel. The IBM produces a variety of spatial patterns which qualitatively match patterns observed in a PDE model. The addition of direction-dependent interaction rules exemplifies how directional information transfer within a group of individuals can result in enriched pattern formation. Our individual-based modelling framework reveals the influence that direction-dependent interaction rules such as biological communication can have upon individual movement trajectories and how these trajectories combine to form group patterns.

Effects of G2-checkpoint dynamics on low-dose hyper-radiosensitivity.

In experimental studies, it has been found that certain cell lines are more sensitive to low-dose radiation than would be expected from the classical Linear-Quadratic model (LQ model). In fact, it is frequently observed that cells incur more damage at low dose (say 0.3 Gy) than at higher dose (say 1 Gy). This effect has been termed hyper-radiosensitivity (HRS). The effect depends on the type of cells and on their phase in the cell cycle when radiation is applied. Experiments have shown that the G2-checkpoint plays an important role in the HRS effects. Here we design and analyze a differential equation model for the cell cycle that includes G2-checkpoint dynamics and radiation treatment. We fit the model to surviving fraction data for different cell lines including glioma cells, prostate cancer cells, as well as to cell populations that are enriched in certain phases of the cell cycle. The HRS effect is measured in the literature through [Formula: see text], the ratio of slope [Formula: see text] of the surviving fraction curve at zero dose to slope [Formula: see text] of the corresponding LQ model. We derive an explicit formula for this ratio and we show that it corresponds very closely to experimental observations. Finally, we identify the dependence of this ratio on the surviving fraction at 2 Gy. It was speculated in the literature that such dependence exists. Our theoretical analysis will help to more systematically identify the HRS in cell lines, and opens doors to analyze its use in cancer treatment.

Existence and uniqueness for a coupled PDE model for motor-induced microtubule organization.

Microtubules (MTs) are protein filaments that provide structure to the cytoskeleton of cells and a platform for the movement of intracellular substances. The spatial organization of MTs is crucial for a cell's form and function. MTs interact with a class of proteins called motor proteins that can transport and position individual filaments, thus contributing to overall organization. In this paper, we study the mathematical properties of a coupled partial differential equation (PDE) model, introduced by White et al. in 2015, that describes the motor-induced organization of MTs. The model consists of a nonlinear coupling of a hyperbolic PDE for bound motor proteins, a parabolic PDE for unbound motor proteins, and a transport equation for MT dynamics. We locally smooth the motor drift velocity in the equation for bound motor proteins. The mollification is not only critical for the analysis of the model, but also adds biological realism. We then use a Banach Fixed Point argument to show local existence and uniqueness of mild solutions. We highlight the applicability of the model by showing numerical simulations that are consistent with in vitro experiments.

A reaction-diffusion model for radiation-induced bystander effects.

We develop and analyze a reaction-diffusion model to investigate the dynamics of the lifespan of a bystander signal emitted when cells are exposed to radiation. Experimental studies by Mothersill and Seymour 1997, using malignant epithelial cell lines, found that an emitted bystander signal can still cause bystander effects in cells even 60 h after its emission. Several other experiments have also shown that the signal can persist for months and even years. Also, bystander effects have been hypothesized as one of the factors responsible for the phenomenon of low-dose hyper-radiosensitivity and increased radioresistance (HRS/IRR). Here, we confirm this hypothesis with a mathematical model, which we fit to Joiner's data on HRS/IRR in a T98G glioma cell line. Furthermore, we use phase plane analysis to understand the full dynamics of the signal's lifespan. We find that both single and multiple radiation exposure can lead to bystander signals that either persist temporarily or permanently. We also found that, in an heterogeneous environment, the size of the domain exposed to radiation and the number of radiation exposures can determine whether a signal will persist temporarily or permanently. Finally, we use sensitivity analysis to identify those cell parameters that affect the signal's lifespan and the signal-induced cell death the most.

Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.

Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous.

Microtubule patterning in the presence of stationary motor distributions.

In this paper, we construct a novel nonlocal transport model that describes the evolution of microtubules (MTs) as they interact with stationary distributions of motor proteins. An advection term accounts for directed MT transport (sliding due to motor protein action), and an integral term accounts for reorientation of MTs due to their interactions with cross-linking motor proteins. Simulations of our model show how MT patterns depend on boundary constraints, as well as model parameters that represent motor speed, cross-linking capability (motor activity), and directionality. In large domains, and using motor parameter values consistent with experimentally-derived values, we find that patterns such as asters, vortices, and bundles are able to persist. In vivo, MTs take on aster patterns during interphase and they form bundles in neurons and polarized epithelial cells. Vortex patterns have not been observed in vivo, however, are found in in vitro experiments. In constrained domains, we find that similar patterns form (asters, bundles, and vortices). However, we also find that when two opposing motors are present, anti-parallel bundles are able to form, resembling the mitotic spindle during cell division. This model demonstrates how MT sliding and MT reorientation are sufficient to produce experimentally observed patterns.

Analysis of molecular diffusion by first-passage time variance identifies the size of confinement zones.

The diffusion of receptors within the two-dimensional environment of the plasma membrane is a complex process. Although certain components diffuse according to a random walk model (Brownian diffusion), an overwhelming body of work has found that membrane diffusion is nonideal (anomalous diffusion). One of the most powerful methods for studying membrane diffusion is single particle tracking (SPT), which records the trajectory of a label attached to a membrane component of interest. One of the outstanding problems in SPT is the analysis of data to identify the presence of heterogeneity. We have adapted a first-passage time (FPT) algorithm, originally developed for the interpretation of animal movement, for the analysis of SPT data. We discuss the general application of the FPT analysis to molecular diffusion, and use simulations to test the method against data containing known regions of confinement. We conclude that FPT can be used to identify the presence and size of confinement within trajectories of the receptor LFA-1, and these results are consistent with previous reports on the size of LFA-1 clusters. The analysis of trajectory data for cell surface receptors by FPT provides a robust method to determine the presence and size of confined regions of diffusion.

From cell population models to tumor control probability: including cell cycle effects.

BACKGROUND: Classical expressions for the tumor control probability (TCP) are based on models for the survival fraction of cancer cells after radiation treatment. We focus on the derivation of expressions for TCP from dynamic cell population models. In particular, we derive a TCP formula for a generalized cell population model that includes the cell cycle by considering a compartment of actively proliferating cells and a compartment of quiescent cells, with the quiescent cells being less sensitive to radiation than the actively proliferating cells. METHODS: We generalize previously derived TCP formulas of Zaider and Minerbo and of Dawson and Hillen to derive a TCP formula from our cell population model. We then use six prostate cancer treatment protocols as a case study to show how our TCP formula works and how the cell cycle affects the tumor treatment. RESULTS: The TCP formulas of Zaider-Minerbo and of Dawson-Hillen are special cases of the TCP formula presented here. The former one represents the case with no quiescent cells while the latter one assumes that all newly born cells enter a quiescent cell phase before becoming active. From our case study, we observe that inclusion of the cell cycle lowers the TCP. CONCLUSION: The cell cycle can be understood as the sequestration of cells in the quiescent compartment, where they are less sensitive to radiation. We suggest that our model can be used in combination with synchronization methods to optimize treatment timing.

Nucleoplasmic beta-actin exists in a dynamic equilibrium between low-mobility polymeric species and rapidly diffusing populations.

Beta-actin, once thought to be an exclusively cytoplasmic protein, is now known to have important functions within the nucleus. Nuclear beta-actin associates with and functions in chromatin remodeling complexes, ribonucleic acid polymerase complexes, and at least some ribonucleoproteins. Proteins involved in regulating actin polymerization are also found in the interphase nucleus. We define the dynamic properties of nuclear actin molecules using fluorescence recovery after photobleaching. Our results indicate that actin and actin-containing complexes are reduced in their mobility through the nucleoplasm diffusing at approximately 0.5 microm2 s(-1). We also observed that approximately 20% of the total nuclear actin pool has properties of polymeric actin that turns over rapidly. This pool could be detected in endogenous nuclear actin by using fluorescent polymeric actin binding proteins and was sensitive to drugs that alter actin polymerization. Our results validate previous reports of polymeric forms of nuclear actin observed in fixed specimens and reveal that these polymeric forms are very dynamic.

Kir6.2 polymorphisms sensitize beta-cell ATP-sensitive potassium channels to activation by acyl CoAs: a possible cellular mechanism for increased susceptibility to type 2 diabetes?

The commonly occurring E23K and I337V Kir6.2 polymorphisms in the ATP-sensitive potassium (KATP) channel are more frequent in Caucasian type 2 diabetic populations. However, the underlying cellular mechanisms contributing to the pathogenesis of type 2 diabetes remain uncharacterized. Chronic elevation of plasma free fatty acids observed in obese and type 2 diabetic subjects leads to cytosolic accumulation of long-chain acyl CoAs (LC-CoAs) in pancreatic beta-cells. We postulated that the documented stimulatory effects of LC-CoAs on KATP channels might be enhanced in polymorphic KATP channels. Patch-clamp experiments were performed on inside-out patches containing recombinant KATP channels (Kir6.2/SUR1) to record macroscopic currents. KATP channels containing Kir6.2 (E23K/I337V) showed significantly increased activity in response to physiological palmitoyl-CoA concentrations (100-1,000 nmol/l) compared with wild-type KATP channels. At physiological intracellular ATP concentrations (mmol/l), E23K/I337V polymorphic KATP channels demonstrated significantly enhanced activity in response to palmitoyl-CoA. The observed increase in KATP channel activity may result in multiple defects in glucose homeostasis, including impaired insulin and glucagon-like peptide-1 secretion and increased glucagon release. In summary, these results suggest that the E23K/I337V polymorphism may have a diabetogenic effect via increased KATP channel activity in response to endogenous levels of LC-CoAs in tissues involved in the maintenance of glucose homeostasis.

Using FRAP and mathematical modeling to determine the in vivo kinetics of nuclear proteins.

Fluorescence recovery after photobleaching (FRAP) has become a popular technique to investigate the behavior of proteins in living cells. Although the technique is relatively old, its application to studying endogenous intracellular proteins in living cells is relatively recent and is a consequence of the newly developed fluorescent protein-based living cell protein tags. This is particularly true for nuclear proteins, in which endogenous protein mobility has only recently been studied. Here we examine the experimental design and analysis of FRAP experiments. Mathematical modeling of FRAP data enables the experimentalist to extract information such as the association and dissociation constants, distribution of a protein between mobile and immobilized pools, and the effective diffusion coefficient of the molecule under study. As experimentalists begin to dissect the relative influence of protein domains within individual proteins, this approach will allow a quantitative assessment of the relative influences of different molecular interactions on the steady-state distribution and protein function in vivo.