Andrzej Swierniak

Gene Expression Profile of Papillary Thyroid Cancer: Sources of Variability and Diagnostic Implications

The study looked for an optimal set of genes differentiating between papillary thyroid cancer (PTC) and normal thyroid tissue and assessed the sources of variability in gene expression profiles. The analysis was done by oligonucleotide microarrays (GeneChip HG-U133A) in 50 tissue samples taken intraoperatively from 33 patients (23 PTC patients and 10 patients with other thyroid disease). In the initial group of 16 PTC and 16 normal samples, we assessed the sources of variability in the gene expression profile by singular value decomposition which specified three major patterns of variability. The first and the most distinct mode grouped transcripts differentiating between tumor and normal tissues. Two consecutive modes contained a large proportion of immunity-related genes. To generate a multigene classifier for tumor-normal difference, we used support vector machines-based technique (recursive feature replacement). It included the following 19 genes: DPP4, GJB3, ST14, SERPINA1, LRP4, MET, EVA1, SPUVE, LGALS3, HBB, MKRN2, MRC2, IGSF1, KIAA0830, RXRG, P4HA2, CDH3, IL13RA1, and MTMR4, and correctly discriminated 17 of 18 additional PTC/normal thyroid samples and all 16 samples published in a previous microarray study. Selected novel genes (LRP4, EVA1, TMPRSS4, QPCT, and SLC34A2) were confirmed by Q-PCR. Our results prove that the gene expression signal of PTC is easily detectable even when cancer cells do not prevail over tumor stroma. We indicate and separate the confounding variability related to the immune response. Finally, we propose a potent molecular classifier able to discriminate between PTC and nonmalignant thyroid in more than 90% of investigated samples.

Optimal control problems arising in cell‐cycle‐specific cancer chemotherapy

We explore mathematical properties of models of cancer chemotherapy including cell‐cycle dependence. Using the mathematical methods of control theory, we demonstrate two assertions of interest for the biomedical community: 1 Periodic chemotherapy protocols are close to the optimum for a wide class of models and have additional favourable properties. 2 Two possible approaches, (a) to minimize the final count of malignant cells and the cumulative effect of the drug on normal cells, or (b) to maximize the final count of normal cells and the cumulative effect of the drug on malignant cells, lead to similar principles of optimization.

A multi-gene approach to differentiate papillary thyroid carcinoma from benign lesions: gene selection using support vector machines with bootstrapping

Selection of novel molecular markers is an important goal of cancer genomics studies. The aim of our analysis was to apply the multivariate bioinformatical tools to rank the genes – potential markers of papillary thyroid cancer (PTC) according to their diagnostic usefulness. We also assessed the accuracy of benign/malignant classification, based on gene expression profiling, for PTC. We analyzed a 180-array dataset (90 HG-U95A and 90 HG-U133A oligonucleotide arrays), which included a collection of 57 PTCs, 61 benign thyroid tumors, and 62 apparently normal tissues. Gene selection was carried out by the support vector machines method with bootstrapping, which allowed us 1) ranking the genes that were most important for classification quality and appeared most frequently in the classifiers (bootstrap-based feature ranking, BBFR); 2) ranking the samples, and thus detecting cases that were most difficult to classify (bootstrap-based outlier detection). The accuracy of PTC diagnosis was 98.5% for a 20-gene classifier, its 95% confidence interval (CI) was 95.9–100%, with the lower limit of CI exceeding 95% already for five genes. Only 5 of 180 samples (2.8%) were misclassified in more than 10% of bootstrap iterations. We specified 43 genes which are most suitable as molecular markers of PTC, among them some well-known PTC markers (MET, fibronectin 1, dipeptidylpeptidase 4, or adenosine A1 receptor) and potential new ones (UDP-galactose-4-epimerase, cadherin 16, gap junction protein 3, sushi, nidogen, and EGF-like domains 1, inhibitor of DNA binding 3, RUNX1, leiomodin 1, F-box protein 9, and tripartite motif-containing 58). The highest ranking gene, metallophosphoesterase domain-containing protein 2, achieved 96.7% of the maximum BBFR score.

Mathematical modeling as a tool for planning anticancer therapy

We review a large volume of literature concerning mathematical models of cancer therapy, oriented towards optimization of treatment protocols. The review, although partly idiosyncratic, covers such major areas of therapy optimization as phase-specific chemotherapy, antiangiogenic therapy and therapy under drug resistance. We start from early cell cycle progression models, very simple but admitting explicit mathematical solutions, based on methods of control theory. We continue with more complex models involving evolution of drug resistance and pharmacokinetic and pharmacodynamic effects. Then, we consider two more recent areas: angiogenesis of tumors and molecular signaling within and among cells. We discuss biological background and mathematical techniques of this field, which has a large although only partly realized potential for contributing to cancer treatment.

Radiation-induced micronucleus frequency in peripheral blood lymphocytes is correlated with normal tissue damage in patients with cervical carcinoma undergoing radiotherapy.

Abstract Widel, M., Jedrus, S., Lukaszczyk, B., Raczek-Zwierzycka, K. and Swierniak, A. Radiation-Induced Micronucleus Frequency in Peripheral Blood Lymphocytes is Correlated with Normal Tissue Damage in Patients with Cervical Carcinoma Undergoing Radiotherapy. Radiat. Res. 159, 713–721 (2003). In an effort to find a test to predict the response of normal tissue to radiotherapy, the lymphocyte micronucleus assay was used on blood samples from patients with cervical carcinoma. Peripheral blood samples from 55 patients with advanced-stage (II B–IV B) cervical carcinoma were obtained before radiotherapy. The patients were treated with external-beam radiotherapy followed by high-dose-rate brachytherapy. Acute and late normal tissue reactions were scored and correlated with the micronucleus frequency in lymphocytes after irradiation with 4 Gy in vitro. Great interindividual variability was observed in the radiation-induced lymphocyte micronucleus frequency, especially at 4 Gy. The mean number of micronuclei per 100 binucleated cells in cells irradiated with 4 Gy in vitro was significantly higher in samples from patients who suffered from acute and/or late normal tissue reactions than in those from patients with no reactions (51.0 ± 17.7 and 29.6 ± 10.1, respectively). A significant correlation was also found between the micronucleus frequency at 4 Gy and the severity of acute reactions and late reactions. However, the overlap between the micronucleus frequencies of patients with high-grade late normal tissue reactions and low-grade reactions is too great to recommend the micronucleus assay in its present form for routine clinical application.

Control Theory Approach to Cancer Chemotherapy: Benefiting from Phase Dependence and Overcoming Drug Resistance

Two major obstacles against successful chemotherapy of cancer are (1) cell-cycle-phase dependence of treatment, and (2) emergence of resistance of cancer cells to cytotoxic agents. One way to understand and overcome these two problems is to apply optimal control theory to mathematical models of cell cycle dynamics. These models should include division of the cell cycle into subphases and/or the mechanisms of drug resistance. We review our results in mathematical modeling and control of the cell cycle and of the mechanisms of gene amplification (related to drug resistance), and estimation of parameters of the constructed models.

Bystander Effects Induced by Medium From Irradiated Cells: Similar Transcriptome Responses in Irradiated and Bystander K562 Cells

PURPOSE Cells exposed to ionizing radiation release factors that induce deoxyribonucleic acid damage, chromosomal instability, apoptosis, and changes in the proliferation rate of neighboring unexposed cells, phenomena known as bystander effects. This work analyzes and compares changes in global transcript levels induced by direct irradiation and by bystander effects in K562 (human erythroleukemia) cells. METHODS AND MATERIALS Cells were X-irradiated with 4 Gy or transferred into culture medium collected from cells 1 h after irradiation (irradiation-conditioned medium). Global transcript profiles were assessed after 36 h of growth by use of Affymetrix microarrays (Affymetrix, Santa Clara, CA) and the kinetics of change of selected transcripts by quantitative reverse transcriptase-polymerase chain reaction. RESULTS The level of the majority (72%) of transcripts changed similarly (increase, decrease, or no change) in cells grown in irradiation-conditioned medium or irradiated, whereas only 0.6% showed an opposite response. Transcript level changes in bystander and irradiated cells were significantly different from those in untreated cells grown for the same amount of time and were confirmed by quantitative reverse transcriptase-polymerase chain reaction for selected genes. Signaling pathways in which the highest number of transcripts changed in both conditions were found in the following groups: neuroactive ligand-receptor, cytokine-cytokine receptor interaction, Janus Kinase-Signal Transducers and Activators of Transcription (JAK-STAT) and Mitogen-Activated Protein Kinase (MAPK) In control cells more transcripts were downregulated than in irradiated and bystander cells with transcription factors YBX1 and STAT5B, heat shock protein HSPA1A, and ribonucleic acid helicase DDX3X as examples. CONCLUSIONS The transcriptomes of cells grown in medium from X-irradiated cells or directly irradiated show very similar changes. Signals released by irradiated cells may cause changes in the transcriptome of neighboring cells that sustain their survival.

Adjoint Systems for Models of Cell Signaling Pathways and their Application to Parameter Fitting

The paper concerns the problem of fitting mathematical models of cell signaling pathways. Such models frequently take the form of sets of nonlinear ordinary differential equations. While the model is continuous in time, the performance index used in the fitting procedure, involves measurements taken at discrete time moments. Adjoint sensitivity analysis is a tool, which can be used for finding the gradient of a performance index in the space of parameters of the model. In the paper a structural formulation of adjoint sensitivity analysis called the Generalized Backpropagation Through Time (GBPTT) is used. The method is especially suited for hybrid, continuous-discrete time systems. As an example we use the mathematical model of the NF-kB regulatory module, which plays a major role in the innate immune response in animals.

On controllability with respect to the expectation of discrete time jump linear systems

Abstract In this paper we consider a problem of controllability of discrete time linear systems endowed with randomly jumping parameters which can be described by a finite state Markov chain. Necessary and sufficient conditions for existence of a control which governs the expectation of the state of the system from any initial condition to a given target value at a given time are presented. Comparison with other definitions of controllability for such systems is also done.

Advanced Technologies for Intelligent Systems of National Border Security

One of the worlds leading problems in the field of national security is protection of borders and borderlands. This book addresses multiple issues on advanced innovative methods of multi-level control of both ground (UGVs) and aerial drones (UAVs). Those objects combined with innovative algorithms become autonomous objects capable of patrolling chosen borderland areas by themselves and automatically inform the operator of the system about potential place of detection of a specific incident. This is achieved by using sophisticated methods of generation of non-collision trajectory for those types of objects and enabling automatic integration of both ground and aerial unmanned vehicles. The topics included in this book also cover presentation of complete information and communication technology (ICT) systems capable of control, observation and detection of various types of incidents and threats. This book is a valuable source of information for constructors and developers of such solutions for uniformed services. Scientists and researchers involved in computer vision, image processing, data fusion, control algorithms or IC can find many valuable suggestions and solutions. Multiple challenges for such systems are also presented.