Treatment of evolving cancers will require dynamic decision support.

Cancer research has traditionally focused on developing new agents, but an underexplored question is that of the dose and frequency of existing drugs. Based on the modus operandi established in the early days of chemotherapies, most drugs are administered according to predetermined schedules that seek to deliver the maximum tolerated dose and are only adjusted for toxicity. However, we believe that the complex, evolving nature of cancer requires a more dynamic and personalized approach. Chronicling the milestones of the field, we show that the impact of schedule choice crucially depends on processes driving treatment response and failure. As such, cancer heterogeneity and evolution dictate that a one-size-fits-all solution is unlikely-instead, each patient should be mapped to the strategy that best matches their current disease characteristics and treatment objectives (i.e. their 'tumorscape'). To achieve this level of personalization, we need mathematical modeling. In this perspective, we propose a five-step 'Adaptive Dosing Adjusted for Personalized Tumorscapes (ADAPT)' paradigm to integrate data and understanding across scales and derive dynamic and personalized schedules. We conclude with promising examples of model-guided schedule personalization and a call to action to address key outstanding challenges surrounding data collection, model development, and integration.

Connectomic Basis for Tremor Control in Stereotactic Radiosurgical Thalamotomy.

BACKGROUND AND PURPOSE: Given the increased use of stereotactic radiosurgical thalamotomy and other ablative therapies for tremor, new biomarkers are needed to improve outcomes. Using resting-state fMRI and MR tractography, we hypothesized that a "connectome fingerprint" can predict tremor outcomes and potentially serve as a targeting biomarker for stereotactic radiosurgical thalamotomy. MATERIALS AND METHODS: We evaluated 27 patients who underwent unilateral stereotactic radiosurgical thalamotomy for essential tremor or tremor-predominant Parkinson disease. Percentage postoperative improvement in the contralateral limb Fahn-Tolosa-Marin Clinical Tremor Rating Scale (TRS) was the primary end point. Connectome-style resting-state fMRI and MR tractography were performed before stereotactic radiosurgery. Using the final lesion volume as a seed, "connectivity fingerprints" representing ideal connectivity maps were generated as whole-brain R-maps using a voxelwise nonparametric Spearman correlation. A leave-one-out cross-validation was performed using the generated R-maps. RESULTS: The mean improvement in the contralateral tremor score was 55.1% (SD, 38.9%) at a mean follow-up of 10.0 (SD, 5.0) months. Structural connectivity correlated with contralateral TRS improvement (r = 0.52; P = .006) and explained 27.0% of the variance in outcome. Functional connectivity correlated with contralateral TRS improvement (r = 0.50; P = .008) and explained 25.0% of the variance in outcome. Nodes most correlated with tremor improvement corresponded to areas of known network dysfunction in tremor, including the cerebello-thalamo-cortical pathway and the primary and extrastriate visual cortices. CONCLUSIONS: Stereotactic radiosurgical targets with a distinct connectivity profile predict improvement in tremor after treatment. Such connectomic fingerprints show promise for developing patient-specific biomarkers to guide therapy with stereotactic radiosurgical thalamotomy.

A novel splice variant of the Excitatory Amino Acid Transporter 5: Cloning, immunolocalization and functional characterization of hEAAT5v in human retina.

Excitatory Amino Acid Transporter 5 (EAAT5) is abundantly expressed by retinal photoreceptors and bipolar cells, where it acts as a slow glutamate transporter and a glutamate-gated chloride channel. The chloride conductance is large enough for EAAT5 to serve as an "inhibitory" glutamate receptor. Our recent work in rodents has shown that EAAT5 is differentially spliced and exists in many variant forms. The chief aim of the present study was to examine whether EAAT5 is also alternately spliced in human retina and, if so, what significance this might have for retinal function in health and disease. Retinal tissues from human donor eyes were used in RT-PCR to amplify the entire coding region of EAAT5. Amplicons of differing sizes were sub-cloned and analysis of sequenced data revealed the identification of wild-type human EAAT5 (hEAAT5) and an abundant alternately spliced form, referred to as hEAAT5v, where the open reading frame is expanded by insertion of an additional exon. hEAAT5v encodes a protein of 619 amino acids and when expressed in COS7 cells, the protein functioned as a glutamate transporter. We raised antibodies that selectively recognized the hEAAT5v protein and have performed immunocytochemistry to demonstrate expression in photoreceptors in human retina. We noted that in retinas afflicted by dry aged-related macular degeneration (AMD), there was a loss of hEAAT5v from the lesioned area and from photoreceptors adjacent to the lesion. We conclude that hEAAT5v protein expression may be perturbed in peri-lesional areas of AMD-afflicted retinas that do not otherwise exhibit evidence of damage. The loss of hEAAT5v could, therefore, represent an early pathological change in the development of AMD and might be involved in its aetiology.

Excitatory amino acid transporter 5 is widely expressed in peripheral tissues.

It is routinely stated in the literature that Excitatory Amino Acid Transporter 5 (EAAT5) is a retina-specific glutamate transporter. EAAT5 is expressed by retinal photoreceptors and bipolar cells, where it serves as a slow transporter and as an inhibitory glutamate receptor, the latter role is due to the gating of a large chloride conductance. The dogma of an exclusively retinal distribution has arisen because Northern blot analyses have previously shown only modest hybridisation in non-retinal tissues. Others have re-interpreted this as indicating that EAAT5 was only present in retinal tissues. However, this view appears to be erroneous; recent evidence demonstrating abundant expression of EAAT5 in rat testis prompted us to re-examine this dogma. A new antibody was developed to an intracellular loop region of rat EAAT5. This new tool, in concert with RT-PCR and sequencing, demonstrated that EAAT5 is widely distributed at the mRNA and protein levels in many non-nervous tissues including liver, kidney, intestine, heart, lung, and skeletal muscle. We conclude that EAAT5 is a widely distributed protein. Whether it functions in all locations as a glutamate transporter, or mainly as a glutamate-gated chloride conductance, remains to be determined.

Investigating prostate cancer tumour-stroma interactions: clinical and biological insights from an evolutionary game.

BACKGROUND: Tumours are made up of a mixed population of different types of cells that include normal structures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under-appreciated therapeutic target. We use observations of primary tumour biology from prostate cancer to extrapolate a mathematical model. Specifically, it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent--in this case the local stromal cells may act to restrain the growth of the cancer; (ii) early in its genesis the tumour acquires a highly malignant phenotype, growing rapidly and displacing the original stromal population (often referred to as small cell prostate cancer)--these less common aggressive tumours are relatively independent of the local microenvironment and (iii) the tumour co-opts the local stroma--taking on a classic stromagenic phenotype where interactions with the local microenvironment are critical to the cancer growth. METHODS: We present an evolutionary game theoretical construct that models the influence of tumour-stroma interactions in driving these outcomes. We consider three characteristic and distinct cellular populations: stromal cells, tumour cells that are self-reliant in terms of microenvironmental factors and tumour cells that depend on the environment for resources, but can also co-opt stroma. RESULTS: Using evolutionary game theory we explore a number of different scenarios that elucidate the impact of tumour-stromal interactions on the dynamics of prostate cancer growth and progression, and how different treatments in the metastatic setting can affect different types of tumours. CONCLUSION: The tumour microenvironment has a crucial role in selecting the traits of the tumour cells that will determine prostate cancer progression. Equally important treatments like hormone therapy affect the selection of these cancer phenotypes making it very important to understand how they impact prostate cancer's somatic evolution.

The biology underlying molecular imaging in oncology: from genome to anatome and back again.

Cancers are complex, evolving, multiscale ecosystems that are characterized by profound spatial and temporal heterogeneity. The interactions in cancer are non-linear in that small changes in one variable can have large changes on another. These multiple interacting phenotypes and spatial scales can best be understood with appropriate mathematical and computational models. Imaging is central to this investigation because it can non-destructively and longitudinally characterize spatial variations in the tumour phenotype and environment so that the system dynamics over time can be captured quantitatively.

Perspectives on tissue interactions in development and disease.

From the morphogenetic movements of the three germ layers during development to the reactive stromal microenvironment in cancer, tissue interactions are vital to maintaining healthy organ morphologic architecture and function. The stromal compartment is thought to be complicit in tumor progression and, as such, represents an opportune target for disease therapies. However, recent developments in our understanding of the diversity of the stromal compartment and the lack of appropriate models to study its relevance in human disease have limited our further understanding of the role of tissue interactions in tumor progression. The failure any model to fully recapitulate the complexities of systemic biology continue to create a higher imperative for incorporating various perspectives into a broader understanding for the ultimate goal of designing interventional therapies. Understanding this potential, this review examines the biological models used to study stromal-epithelial interactions and includes an attempt to incorporate behavioral terminology to define and mathematically model ecological relationships in stromal-epithelial interactions. In addition, the current attempt to incorporate these diverse ecological perspectives into in silico mathematical models through cross-disciplinary coordination is reviewed, which will provide a fresh perspective on defining cell group behavior and tissue ecology in disease and hopefully lead to the generation of new hypotheses to be empirically validated.

Evolution of cell motility in an individual-based model of tumour growth.

Tumour invasion is driven by proliferation and importantly migration into the surrounding tissue. Cancer cell motility is also critical in the formation of metastases and is therefore a fundamental issue in cancer research. In this paper we investigate the emergence of cancer cell motility in an evolving tumour population using an individual-based modelling approach. In this model of tumour growth each cell is equipped with a micro-environment response network that determines the behaviour or phenotype of the cell based on the local environment. The response network is modelled using a feed-forward neural network, which is subject to mutations when the cells divide. With this model we have investigated the impact of the micro-environment on the emergence of a motile invasive phenotype. The results show that when a motile phenotype emerges the dynamics of the model are radically changed and we observe faster growing tumours exhibiting diffuse morphologies. Further we observe that the emergence of a motile subclone can occur in a wide range of micro-environmental growth conditions. Iterated simulations showed that in identical growth conditions the evolutionary dynamics either converge to a proliferating or migratory phenotype, which suggests that the introduction of cell motility into the model changes the shape of fitness landscape on which the cancer cell population evolves and that it now contains several local maxima. This could have important implications for cancer treatments which focus on the gene level, as our results show that several distinct genotypes and critically distinct phenotypes can emerge and become dominant in the same micro-environment.

Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms.

We have studied the metabolic gene-function network in yeast and digital organisms evolved in the artificial life platform Avida. The gene-function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene-function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with Avida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.

Validating genetic risk associations for ovarian cancer through the international Ovarian Cancer Association Consortium.

The search for genetic variants associated with ovarian cancer risk has focused on pathways including sex steroid hormones, DNA repair, and cell cycle control. The Ovarian Cancer Association Consortium (OCAC) identified 10 single-nucleotide polymorphisms (SNPs) in genes in these pathways, which had been genotyped by Consortium members and a pooled analysis of these data was conducted. Three of the 10 SNPs showed evidence of an association with ovarian cancer at P< or =0.10 in a log-additive model: rs2740574 in CYP3A4 (P=0.011), rs1805386 in LIG4 (P=0.007), and rs3218536 in XRCC2 (P=0.095). Additional genotyping in other OCAC studies was undertaken and only the variant in CYP3A4, rs2740574, continued to show an association in the replication data among homozygous carriers: OR(homozygous(hom))=2.50 (95% CI 0.54-11.57, P=0.24) with 1406 cases and 2827 controls. Overall, in the combined data the odds ratio was 2.81 among carriers of two copies of the minor allele (95% CI 1.20-6.56, P=0.017, p(het) across studies=0.42) with 1969 cases and 3491 controls. There was no association among heterozygous carriers. CYP3A4 encodes a key enzyme in oestrogen metabolism and our finding between rs2740574 and risk of ovarian cancer suggests that this pathway may be involved in ovarian carcinogenesis. Additional follow-up is warranted.

Modelling evolutionary cell behaviour using neural networks: application to tumour growth.

In this paper, we present a modelling framework for cellular evolution that is based on the notion that a cell's behaviour is driven by interactions with other cells and its immediate environment. We equip each cell with a phenotype that determines its behaviour and implement a decision mechanism to allow evolution of this phenotype. This decision mechanism is modelled using feed-forward neural networks, which have been suggested as suitable models of cell signalling pathways. The environmental variables are presented as inputs to the network and result in a response that corresponds to the phenotype of the cell. The response of the network is determined by the network parameters, which are subject to mutations when the cells divide. This approach is versatile as there are no restrictions on what the input or output nodes represent, they can be chosen to represent any environmental variables and behaviours that are of importance to the cell population under consideration. This framework was implemented in an individual-based model of solid tumour growth in order to investigate the impact of the tissue oxygen concentration on the growth and evolutionary dynamics of the tumour. Our results show that the oxygen concentration affects the tumour at the morphological level, but more importantly has a direct impact on the evolutionary dynamics. When the supply of oxygen is limited we observe a faster divergence away from the initial genotype, a higher population diversity and faster evolution towards aggressive phenotypes. The implementation of this framework suggests that this approach is well suited for modelling systems where evolution plays an important role and where a changing environment exerts selection pressure on the evolving population.

Latitudinal and cold-tolerance variation associate with DNA repeat-number variation in the hsr-omega RNA gene of Drosophila melanogaster.

An 8-bp deletion in the hsr-omega heat-stress gene of Drosophila melanogaster has previously been associated with latitude, and with heat tolerance that decreases with latitude. Here we report a second polymorphic site, at the 3'-end of hsr-omega, at which multiple alleles segregate in natural populations for copy number of a approximately 280 bp tandem repeat. On each of 3 consecutive years (2000, 2001 and 2002) among populations sampled along the Australian eastern coast, repeat number was negatively associated with latitude. Neither altitudinal association was detected in 2002 when five high-altitude sites were included, nor was a robust association detected with local temperature or rainfall measures. Although in a large number of family lines, derived from a population located centrally in the latitudinal transect, no association between hsr-omega repeat number and heat tolerance occurred, a negative association of repeat number with cold tolerance was detected. As cold tolerance also exhibits latitudinal clines we examined a set of cold-tolerant populations derived by selection and found both reduced repeat number and low constitutive levels of the omega-n repeat-bearing transcript. In a sample from the central population, linkage disequilibrium was measured between repeat number and linked markers that also cline latitudinally. However, such disequilibrium could not account for the cline in repeat number or tolerance associations. Finally, during adult recovery from cold exposure a large increase occurred in tissue levels of the omega-c transcript. Together these data suggest that a latitudinal cline in hsr-omega repeat number influences cold-tolerance variation in this species.

How informed is consent in a modern ENT department.

The Department of Health issued a model consent form for use throughout the NHS from the 1st April 2002. Details of benefits and serious or frequent risks should be included on the form. We undertook a study to identify what proportion of complications from otolaryngology procedures were being recorded. Local morbidity and mortality records and case notes were examined from March to November 2004. Complications were identified and recorded. The consent forms for these operations were examined to identify if these complications had been recorded on the form prior to surgery. Complications were classified as "serious", causing significant morbidity or increasing length of hospital stay or "frequent", occurring in 1% or more of cases. A total of 2,978 operations were performed between March and November 2004. Seventy complications were identified in 60 patients (2% of operated patients). Twenty-three complications were not recorded on the consent forms in 20 (33%) patients. A total of 67% of all the complications were documented on the form as potential problems resulting from planned operations. Seven (74%) of complications that occurred but were not recorded on the consent forms were judged as "serious" or "frequent". A significant proportion of serious or frequent complications are not being documented on the national consent forms before otolaryngological procedures and may not have been discussed. This may reflect a lack of openness during the consent process. In the current medical climate, this has serious ethical and medico-legal ramifications. It may also reflect a problem with the form and a need for a re-think of its design.

A hybrid cellular automaton model of clonal evolution in cancer: the emergence of the glycolytic phenotype.

We present a cellular automaton model of clonal evolution in cancer aimed at investigating the emergence of the glycolytic phenotype. In the model each cell is equipped with a micro-environment response network that determines the behaviour or phenotype of the cell based on the local environment. The response network is modelled using a feed-forward neural network, which is subject to mutations when the cells divide. This implies that cells might react differently to the environment and when space and nutrients are limited only the fittest cells will survive. With this model we have investigated the impact of the environment on the growth dynamics of the tumour. In particular, we have analysed the influence of the tissue oxygen concentration and extra-cellular matrix density on the dynamics of the model. We found that the environment influences both the growth and the evolutionary dynamics of the tumour. For low oxygen concentration we observe tumours with a fingered morphology, while increasing the matrix density gives rise to more compact tumours with wider fingers. The distribution of phenotypes in the tumour is also affected, and we observe that the glycolytic phenotype is most likely to emerge in a poorly oxygenated tissue with a high matrix density. Our results suggest that it is the combined effect of the oxygen concentration and matrix density that creates an environment where the glycolytic phenotype has a growth advantage and consequently is most likely to appear.

Obstructive sleep apnoea adenotonsillectomy in children: when to refer to a centre with a paediatric intensive care unit?

OBJECTIVE: To identify regional surgical referral patterns for adenotonsillectomy in children with obstructive sleep apnoea to our tertiary centre with paediatric intensive care unit facilities and to establish guidelines for elective paediatric intensive care unit referral and admission. METHODS: Two methods were used. A questionnaire was sent to ENT consultants in five surrounding hospitals with no in-house paediatric intensive care facilities. The second was a prospective observational study undertaken in our tertiary centre for a sub-set of patients undergoing obstructive sleep apnoea adenotonsillectomy between January 2002 and February 2005. These children were considered high risk as judged clinically by an ENT surgeon. Most had obstructive sleep apnoea and a co-morbidity. Otherwise healthy children with simple obstructive sleep apnoea were excluded. RESULTS: 15 out of 20 consultants responded to the questionnaire. Four referred on the grounds of clinical history, five referred based on pulse oximetry, nine referred syndromal children and four did not refer electively. Of the 49 high risk patients operated on, only 12 required paediatric intensive care admission with no emergency paediatric intensive care admissions. No otherwise healthy children with uncomplicated obstructive sleep apnoea symptoms required paediatric intensive care admission during the study period. CONCLUSION: There was no regional consensus regarding paediatric intensive care unit referral for obstructive sleep apnoea adenotonsillectomy. Clinical judgement without complex sleep studies by those experienced in this area was sufficient to detect complicated cases of obstructive sleep apnoea with co-morbidity requiring paediatric intensive care.

Stability analysis of a hybrid cellular automaton model of cell colony growth.

Cell colonies of bacteria, tumor cells, and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell colony growth. In the model the growth of the colony is limited by a nutrient that is consumed by the cells and which inhibits cell division if it falls below a certain threshold. Using this model we have investigated how the nutrient consumption rate of the cells affects the growth dynamics of the colony. We found that for low consumption rates the colony takes on an Eden-like morphology, while for higher consumption rates the morphology of the colony is branched with a fractal geometry. These findings are in agreement with previous results, but the simplicity of the model presented here allows for a linear stability analysis of the system. By observing that the local growth of the colony is proportional to the flux of the nutrient we derive an approximate dispersion relation for the growth of the colony interface. This dispersion relation shows that the stability of the growth depends on how far the nutrient penetrates into the colony. For low nutrient consumption rates the penetration distance is large, which stabilizes the growth, while for high consumption rates the penetration distance is small, which leads to unstable branched growth. When the penetration distance vanishes the dispersion relation is reduced to the one describing Laplacian growth without ultra-violet regularization. The dispersion relation was verified by measuring how the average branch width depends on the consumption rate of the cells and shows good agreement between theory and simulations.

An evolutionary hybrid cellular automaton model of solid tumour growth.

We propose a cellular automaton model of solid tumour growth, in which each cell is equipped with a micro-environment response network. This network is modelled using a feed-forward artificial neural network, that takes environmental variables as an input and from these determines the cellular behaviour as the output. The response of the network is determined by connection weights and thresholds in the network, which are subject to mutations when the cells divide. As both available space and nutrients are limited resources for the tumour, this gives rise to clonal evolution where only the fittest cells survive. Using this approach we have investigated the impact of the tissue oxygen concentration on the growth and evolutionary dynamics of the tumour. The results show that the oxygen concentration affects the selection pressure, cell population diversity and morphology of the tumour. A low oxygen concentration in the tissue gives rise to a tumour with a fingered morphology that contains aggressive phenotypes with a small apoptotic potential, while a high oxygen concentration in the tissue gives rise to a tumour with a round morphology containing less evolved phenotypes. The tissue oxygen concentration thus affects the tumour at both the morphological level and on the phenotype level.