Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores

In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.     

Plaque imaging and characterization using magnetic resonance imaging: towards molecular assessment

Identification of high-risk atherosclerotic lesions prone to rupture and thrombosis may greatly decrease the morbidity and mortality associated with atherosclerosis. High-resolution magnetic resonance imaging (MRI) has recently emerged as one of the most promising techniques for the non-invasive study of atherothrombotic disease, as it can characterize plaque composition and monitor its progression. The development of MRI contrast agents that specifically target components of the atherosclerotic plaque may enable non-invasive detection of high-risk lesions. This review discusses the use of high-resolution MRI for plaque detection and characterization and the potentials of "Molecular Imaging" using a variety of molecules present in atherosclerotic plaques that may serve as targets for specific contrast agents to allow the identification of high-risk atherosclerotic lesions in-vivo. Ultimately, such agents may enable treatment of "high-risk" patients prior to lesion progression and occurrence of complications.     

Compressive mechanical properties of atherosclerotic plaques—Indentation test to characterise the local anisotropic behaviour

Accurate material models and associated parameters of atherosclerotic plaques are crucial for reliable biomechanical plaque prediction models. These biomechanical models have the potential to increase our understanding of plaque progression and failure, possibly improving risk assessment of plaque rupture, which is the main cause of ischaemic strokes and myocardial infarction. However, experimental biomechanical data on atherosclerotic plaque tissue is scarce and shows a high variability. In addition, most of the biomechanical models assume isotropic behaviour of plaque tissue, which is a general over-simplification. This review discusses the past and the current literature that focus on mechanical properties of plaque derived from compression experiments, using unconfined compression, micro-indentation or nano-indentation. Results will be discussed and the techniques will be mutually compared. Thereafter, an in-house developed indentation method combined with an inverse finite element method is introduced, allowing analysis of the local anisotropic mechanical properties of atherosclerotic plaques. The advantages and limitations of this method will be evaluated and compared to other methods reported in literature.     

Atherosclerotic Plaque Destabilization in Mice: A Comparative Study

Atherosclerosis-associated diseases are the main cause of mortality and morbidity in western societies. The progression of atherosclerosis is a dynamic process evolving from early to advanced lesions that may become rupture-prone vulnerable plaques. Acute coronary syndromes are the clinical manifestation of life-threatening thrombotic events associated with high-risk vulnerable plaques. Hyperlipidemic mouse models have been extensively used in studying the mechanisms controlling initiation and progression of atherosclerosis. However, the understanding of mechanisms leading to atherosclerotic plaque destabilization has been hampered by the lack of proper animal models mimicking this process. Although various mouse models generate atherosclerotic plaques with histological features of human advanced lesions, a consensus model to study atherosclerotic plaque destabilization is still lacking. Hence, we studied the degree and features of plaque vulnerability in different mouse models of atherosclerotic plaque destabilization and find that the model based on the placement of a shear stress modifier in combination with hypercholesterolemia represent with high incidence the most human like lesions compared to the other models.     

Mouse models of atherosclerosis: explaining critical roles of lipid metabolism and inflammation

Atherosclerosis is the most common cause of death globally. It is a complex disease involving morphological and cellular changes in vascular walls. Studying molecular mechanism of the disease is hindered by disease complexity and lack of robust noninvasive diagnostics in human. Mouse models are the most popular animal models that allow researchers to study the mechanism of disease progression. In this review we discuss the advantage and development of mouse as a model for atherosclerotic research. Along with commonly used models, this review discusses strains that are used to study the role of two critical processes associated with the disease—lipid metabolism and inflammation.     

Estimation in a semi-Markov transformation model

Semi-Markov and modulated renewal processes provide a large class of multi-state models which can be used for analysis of longitudinal failure time data. In biomedical applications, models of this kind are often used to describe evolution of a disease and assume that patient may move among a finite number of states representing different phases in the disease progression. Several authors proposed extensions of the proportional hazard model for regression analysis of these processes. In this paper, we consider a general class of censored semi-Markov and modulated renewal processes and propose use of transformation models for their analysis. Special cases include modulated renewal processes with interarrival times specified using transformation models, and semi-Markov processes with with one-step transition probabilities defined using copula-transformation models. We discuss estimation of finite and infinite dimensional parameters and develop an extension of the Gaussian multiplier method for setting confidence bands for transition probabilities and related parameters. A transplant outcome data set from the Center for International Blood and Marrow Transplant Research is used for illustrative purposes.     

Hemodynamic Characteristics of the Vertebrobasilar System Analyzed Using MRI-Based Models

The vertebrobasilar system (VBS) is unique in human anatomy in that two arteries merge into a single vessel, and it is especially important because it supplies the posterior circulation of the brain. Atherosclerosis develops in this region, and atherosclerotic plaques in the vertebrobasilar confluence can progress with catastrophic consequences, including artery occlusion. Quantitative assessments of the flow characteristics in the VBS could elucidate the factors that influence flow patterns in this confluence, and deviations from normal patterns might then be used to predict locations to monitor for potential pathological changes, to detect early signs of disease, and to evaluate treatment options and efficacy. In this study, high-field MRI was used in conjunction with computational fluid dynamics (CFD) modeling to investigate the hemodynamics of subject-specific confluence models (n = 5) and to identify different geometrical classes of vertebrobasilar systems (n = 12) of healthy adult subjects. The curvature of the vessels and their mutual orientation significantly affected flow parameters in the VBS. The basilar artery geometry strongly influenced both skewing of the velocity profiles and the wall shear stress distributions in the VBS. All five subjects modeled possessed varying degrees of vertebral asymmetry, and helical flow was observed in four cases, suggesting that factors other than vertebral asymmetry influence mixing of the vertebral artery flow contributions. These preliminary studies verify that quantitative, MR imaging techniques in conjunction with subject-specific CFD models of healthy adult subjects may be used to characterize VBS hemodynamics and to predict flow features that have been related to the initiation and development of atherosclerosis in large arteries. This work represents an important first step towards applying this approach to study disease initiation and progression in the VBS.     

Cumulative disease progression models for cross‐sectional data: A review and comparison

A better understanding of disease progression is beneficial for early diagnosis and appropriate individual therapy. Many different approaches for statistical modelling of cumulative disease progression have been proposed in the literature, including simple path models up to complex restricted Bayesian networks. Important fields of application are diseases such as cancer and HIV. Tumour progression is measured by means of chromosome aberrations, whereas people infected with HIV develop drug resistances because of genetic changes of the HI‐virus. These two very different diseases have typical courses of disease progression, which can be modelled partly by consecutive and partly by independent steps. This paper gives an overview of the different progression models and points out their advantages and drawbacks. Different models are compared via simulations to analyse how they work if some of their assumptions are violated. In a simulation study, we evaluate how models perform in terms of fitting induced multivariate probability distributions and topological relationships. We often find that the true model class used for generating data is outperformed by either a less or a more complex model class. The more flexible conjunctive Bayesian networks can be used to fit oncogenetic trees, whereas mixtures of oncogenetic trees with three tree components can be well fitted by mixture models with only two tree components.     

Mouse models in neurological disorders: Applications of non-invasive imaging

Neuroimaging techniques represent powerful tools to assess disease-specific cellular, biochemical and molecular processes non-invasively in vivo. Besides providing precise anatomical localisation and quantification, the most exciting advantage of non-invasive imaging techniques is the opportunity to investigate the spatial and temporal dynamics of disease-specific functional and molecular events longitudinally in intact living organisms, so called molecular imaging (MI). Combining neuroimaging technologies with in vivo models of neurological disorders provides unique opportunities to understand the aetiology and pathophysiology of human neurological disorders. In this way, neuroimaging in mouse models of neurological disorders not only can be used for phenotyping specific diseases and monitoring disease progression but also plays an essential role in the development and evaluation of disease-specific treatment approaches. In this way MI is a key technology in translational research, helping to design improved disease models as well as experimental treatment protocols that may afterwards be implemented into clinical routine. The most widely used imaging modalities in animal models to assess in vivo anatomical, functional and molecular events are positron emission tomography (PET), magnetic resonance imaging (MRI) and optical imaging (OI). Here, we review the application of neuroimaging in mouse models of neurodegeneration (Parkinson's disease, PD, and Alzheimer's disease, AD) and brain cancer (glioma).     

A Human Ex Vivo Atherosclerotic Plaque Model to Study Lesion Biology

Atherosclerosis is a chronic inflammatory disease of the vasculature. There are various methods to study the inflammatory compound in atherosclerotic lesions. Mouse models are an important tool to investigate inflammatory processes in atherogenesis, but these models suffer from the phenotypic and functional differences between the murine and human immune system. In vitro cell experiments are used to specifically evaluate cell type-dependent changes caused by a substance of interest, but culture-dependent variations and the inability to analyze the influence of specific molecules in the context of the inflammatory compound in atherosclerotic lesions limit the impact of the results. In addition, measuring levels of a molecule of interest in human blood helps to further investigate its clinical relevance, but this represents systemic and not local inflammation. Therefore, we here describe a plaque culture model to study human atherosclerotic lesion biology ex vivo. In short, fresh plaques are obtained from patients undergoing endarterectomy or coronary artery bypass grafting and stored in RPMI medium on ice until usage. The specimens are cut into small pieces followed by random distribution into a 48-well plate, containing RPMI medium in addition to a substance of interest such as cytokines or chemokines alone or in combination for defined periods of time. After incubation, the plaque pieces can be shock frozen for mRNA isolation, embedded in Paraffin or OCT for immunohistochemistry staining or smashed and lysed for western blotting. Furthermore, cells may be isolated from the plaque for flow cytometry analysis. In addition, supernatants can be collected for protein measurement by ELISA. In conclusion, the presented ex vivo model opens the possibility to further study inflammatory lesional biology, which may result in identification of novel disease mechanisms and therapeutic targets.     

An integrated approach using orthogonal analytical techniques to characterize heparan sulfate structure

Heparan sulfate (HS), a glycosaminoglycan present on the surface of cells, has been postulated to have important roles in driving both normal and pathological physiologies. The chemical structure and sulfation pattern (domain structure) of HS is believed to determine its biological function, to vary across tissue types, and to be modified in the context of disease. Characterization of HS requires isolation and purification of cell surface HS as a complex mixture. This process may introduce additional chemical modification of the native residues. In this study, we describe an approach towards thorough characterization of bovine kidney heparan sulfate (BKHS) that utilizes a variety of orthogonal analytical techniques (e.g. NMR, IP-RPHPLC, LC-MS). These techniques are applied to characterize this mixture at various levels including composition, fragment level, and overall chain properties. The combination of these techniques in many instances provides orthogonal views into the fine structure of HS, and in other instances provides overlapping / confirmatory information from different perspectives. Specifically, this approach enables quantitative determination of natural and modified saccharide residues in the HS chains, and identifies unusual structures. Analysis of partially digested HS chains allows for a better understanding of the domain structures within this mixture, and yields specific insights into the non-reducing end and reducing end structures of the chains. This approach outlines a useful framework that can be applied to elucidate HS structure and thereby provides means to advance understanding of its biological role and potential involvement in disease progression. In addition, the techniques described here can be applied to characterization of heparin from different sources.     

Anti-inflammatory drugs and atherosclerosis

PURPOSE OF REVIEW: Inflammation contributes to the formation and progression of atherosclerosis and the therapeutic potential of some anti-inflammatory drugs has been evaluated for possible antiatherosclerotic effects. This review will briefly describe the mechanisms underlying the inflammation-atherosclerosis connection, the effect of various anti-inflammatory therapies on atherosclerotic disease and a sampling of the potential targets and agents under evaluation. RECENT FINDINGS: Some agents with anti-inflammatory properties appear to have beneficial effects on atherosclerosis or subsequent risk for cardiovascular events, while others have been disappointing. The anti-inflammatory actions of statins have been linked retrospectively with their favorable effects on atherosclerosis progression and clinical outcomes. The cardiovascular safety of COX-2 inhibitors is being assessed prospectively in patients with atherosclerosis. Potential new therapeutic agents targeting other inflammatory mechanisms and oxidative stress are being evaluated in animal models and clinical trials. SUMMARY: Due to the contributory inflammatory pathways in atherosclerosis, the properties of existing and novel anti-inflammatory agents are being carefully and actively evaluated in cardiovascular disease. Advances in our understanding of both atherosclerosis and the inflammatory contributors may play an important role in future strategies to decrease the incidence of atherosclerotic cardiovascular disease.     

A Systematic Model Specification Procedure for an Illness-Death Model without Recovery

Multi-state models are a flexible tool for analyzing complex time-to-event problems with multiple endpoints. Compared to the Cox regression model with a single endpoint or a summarizing composite endpoint, they can provide a more detailed insight into the disease process. Furthermore, prognosis can be improved by including information from intermediate events occurring during the course of the disease. Different model variants, options and additional assumptions provide many possibilities, but at the same time complicate the implementation of multi-state techniques. So far, no guiding literature is available to specify a multi-state model systematically. The objective of this work was to set up a general specification procedure for an illness-death model that optimizes the model fit and predictive accuracy by stepwise reduction of the model. As an application example, we reanalyzed data from an observational study of 434 ovarian cancer patients with progression as intermediate and death as absorbing state. The technique is described in general terms and can be applied to other illness-death models without recovery. The clock-reset approach was used, implicating that the time was reset to zero after progression. The non-homogeneous semi-Markov characteristic stated that the present time as well as the time between surgery and progression influenced survival after progression. Covariate effects on transitions were estimated and proportionality of transition baseline hazards was tested. The finally developed model optimized the accuracy of predictions for two simulated patients. This stepwise procedure yields parsimonious but targeted multi-state models with well interpretable coefficients and optimized predictive ability, even for smaller data sets.     

Dissemination of Chlamydia pneumoniae to the vessel wall in atherosclerosis

Heart disease and stroke are the result of atherosclerotic vascular lesions. It is becoming increasingly clear that an infection may be an important initiating component within the atherogenic process. However, in order for the infection to contribute to atherosclerosis, it must first be capable of disseminating to the vessel wall. Chlamydia pneumoniae is an example of an infectious atherogenic stimulus. The present treatise reviews our knowledge concerning dissemination of infectious agents like C. pneumoniae. Three factors can be identified that modulate the severity of the infection in the vascular wall. First, although all vascular cell types appear to be infected with agents like C. pneumoniae, there are differences in the sensitivity to infection amongst these cell types. Second, the lipid environment is important in defining the effects of C. pneumoniae on atherosclerotic disease. Third, the inflammatory/atherosclerotic interaction is influenced by the specific infectious stimuli employed. The in situ atherogenic effects of C. pneumoniae may be specific to this organism and may not occur with related infectious agents like C. trachomatis. Despite the identification of these three factors, controversy exists surrounding specific characteristics of these effects. This may be the result of a plethora of differing experimental conditions (different labs, different lipids, different cell types or lines, and different C. pneumoniae characteristics (infection, dosage, duration, etc.)). Further study of these important phenomena is clearly warranted in view of the potential importance of infection to the atherosclerotic disease.     

Design and evaluation of a chronic EMG multichannel detection system for long-term recordings of hindlimb muscles in behaving mice

Mouse models are commonly used for identifying the behavioral consequences of genetic modifications, progression or recovery from disease or trauma models, and understanding spinal circuitry. Electromyographic recordings (EMGs) are recognized as providing information not possible from standard behavioral analyses involving gross behavioral or kinematic assessments. We describe here a method for recording from relatively large numbers of muscles in behaving mice. We demonstrate the use of this approach for recording from hindlimb muscles bilaterally in intact animals, following spinal cord injury, and during the progression of ALS. This design can be used in a variety of applications in order to characterize the coordination strategies of mice in health and disease.     

Tumor-specific imaging through progression elevated gene-3 promoter-driven gene expression

Molecular-genetic imaging is advancing from a valuable preclinical tool to a guide for patient management. The strategy involves pairing an imaging reporter gene with a complementary imaging agent in a system that can be used to measure gene expression or protein interaction or track gene-tagged cells in vivo. Tissue-specific promoters can be used to delineate gene expression in certain tissues, particularly when coupled with an appropriate amplification mechanism. Here we show that the progression elevated gene-3 (PEG-3) promoter, derived from a rodent gene mediating tumor progression and metastatic phenotypes, can be used to drive imaging reporters selectively to enable detection of micrometastatic disease in mouse models of human melanoma and breast cancer using bioluminescence and radionuclide-based molecular imaging techniques. Because of its strong promoter activity, tumor specificity and capacity for clinical translation, PEG-3 promoter-driven gene expression may represent a practical, new system for facilitating cancer imaging and therapy.     

Dietary Manipulation and Social Isolation Alter Disease Progression in a Murine Model of Coronary Heart Disease

Background

Mice with a deficiency in the HDL receptor SR-BI and low expression of a modified apolipoprotein E gene (SR-BI KO/ApoeR61^h/h) called ‘HypoE’ when fed an atherogenic, ‘Paigen’ diet develop occlusive, atherosclerotic coronary arterial disease (CHD), myocardial infarctions (MI), and heart dysfunction and die prematurely (50% mortality ∼40 days after initiation of this diet). Because few murine models share with HypoE mice these cardinal, human-like, features of CHD, HypoE mice represent a novel, small animal, diet-inducible and genetically tractable model for CHD. To better describe the properties of this model, we have explored the effects of varying the composition and timing of administration of atherogenic diets, as well as social isolation vs. group housing, on these animals.

Methodology/Principal Findings

HypoE mice were maintained on a standard lab chow diet (control) until two months of age. Subsequently they received one of three atherogenic diets (Paigen, Paigen without cholate, Western) or control diet for varying times and were housed in groups or singly, and we determined the plasma cholesterol levels, extent of cardiomegaly and/or survival. The rate of disease progression could be reduced by lowering the severity of the atherogenic diet and accelerated by social isolation. Disease could be induced by Paigen diets either containing or free of cholate. We also established conditions under which CHD could be initiated by an atherogenic diet and then subsequently, by replacing this diet with standard lab chow, hypercholesterolemia could be reduced and progression to early death prevented.

Conclusions/Significance

HypoE mice provide a powerful, surgery-free, diet-‘titratable’ small animal model that can be used to study the onset of recovery from occlusive, atherosclerotic CHD and heart failure due to MI. HypoE mice can be used for the analysis of the effects of environment (diet, social isolation) on a variety of features of cardiovascular disease.     

ApoA-I related DNA polymorphism in humans with coronary heart disease

Summary A genetic analysis of atherosclerotic patients as well as healthy subjects using an apoA-I gene specific probe confirmed that an EcoRI restriction fragment length polymorphism is related to the development of atherosclerosis. Three subjects with severe coronary heart disease were found to be homozygous for a 6.5 kb fragment hybridizing to the apoA-I probe. In the atherosclerotic patient group 44% were heterozygous for this fragment, compared to 9.5% in the control group. The distribution of genotypes in the atherosclerotic and control groups was signficantly different. Among the heterozygous subjects, specific differences were found after digestion of their DNA with Bam HI restriction endonuclease.     

Role of plaque inflammation in acute and recurrent coronary syndromes

Inflammation plays an important role in the initiation, development, progression and complications of atherosclerotic vascular disease. Our present knowledge of the elementary role of inflammation for the onset of plaque rupture in atherosclerotic coronary lesions primarily stems from autopsy studies. However, the introduction of directional coronary atherectomy catheters has provided a unique opportunity to directly investigate the role of inflammation in coronary syndromes. In this report we describe the role of coronary plaque inflammation, as determined by immunohistochemistry, on the presentation of coronary syndromes and on the clinical outcome following percutaneous interventions.     

Graph models of oncogenesis with an application to melanoma

We describe several analytical techniques for use in developing genetic models of oncogenesis including: methods for the selection of important genetic events, construction of graph models (including distance-based trees, branching trees, contingency trees and directed acyclic graph models) from these events and methods for interpretation of the resulting models. The models can be used to make predictions about: which genetic events tend to occur early, which events tend to occur together and the likely order of events. Unlike simple path models of oncogenesis, our models allow dependencies to exist between specific genetic changes and allow for multiple, divergent paths in tumor progression. A variety of genetic events can be used with the graph models including chromosome breaks, losses or gains of large DNA regions, small mutations and changes in methylation. As an application of the techniques, we use a recently published cytogenetic analysis of 206 melanoma cases [Nelson et al. (2000), Cancer Genet. Cytogenet.122, 101-109] to derive graph models for chromosome breaks in melanoma. Among our predictions are: (1) breaks in 6q1 and 1q1 are early events, with 6q1 preferentially occurring first and increasing the probability of a break in 1q1 and (2) breaks in the two sets [1p1, 1p2, 9q1] and [1q1, 7p2, 9p2] tend to occur together. This study illustrates that the application of graph models to genetic data from tumor sets provide new information on the interrelationships among genetic changes during tumor progression.