An engineering perspective on transcription, translation and their regulation.

Information coded in DNA is replicated, modified and transmitted from the origins of protein-based life. Analogies of these processes to information processing, transmission and storage in computer systems is straightforward and can be utilized both in analysis of biological data and in development of biologically based technical systems. Transcription and translation processes are regulated by extremely complex regulatory networks, providing control of cell growth, cell cycle and cellular responses to stress. As such, they constitute engineering control systems exerting their actions at many levels of time scale and spatial organization. This work presents an engineering perspective on DNA-related information processing and biochemical process control  in living cells, followed by a review of two-way crosstalk between engineering and biology.

Multiomics-Based Feature Extraction and Selection for the Prediction of Lung Cancer Survival.

Lung cancer is a global health challenge, hindered by delayed diagnosis and the disease's complex molecular landscape. Accurate patient survival prediction is critical, motivating the exploration of various -omics datasets using machine learning methods. Leveraging multi-omics data, this study seeks to enhance the accuracy of survival prediction by proposing new feature extraction techniques combined with unbiased feature selection. Two lung adenocarcinoma multi-omics datasets, originating from the TCGA and CPTAC-3 projects, were employed for this purpose, emphasizing gene expression, methylation, and mutations as the most relevant data sources that provide features for the survival prediction models. Additionally, gene set aggregation was shown to be the most effective feature extraction method for mutation and copy number variation data. Using the TCGA dataset, we identified 32 molecular features that allowed the construction of a 2-year survival prediction model with an AUC of 0.839. The selected features were additionally tested on an independent CPTAC-3 dataset, achieving an AUC of 0.815 in nested cross-validation, which confirmed the robustness of the identified features.

Mathematical Modeling Support for Lung Cancer Therapy-A Short Review.

The paper presents a review of models that can be used to describe dynamics of lung cancer growth and its response to treatment at both cell population and intracellular processes levels. To address the latter, models of signaling pathways associated with cellular responses to treatment are overviewed. First, treatment options for lung cancer are discussed, and main signaling pathways and regulatory networks are briefly reviewed. Then, approaches used to model specific therapies are discussed. Following that, models of intracellular processes that are crucial in responses to therapies are presented. The paper is concluded with a discussion of the applicability of the presented approaches in the context of lung cancer.

Radiomic signature accurately predicts the risk of metastatic dissemination in late-stage non-small cell lung cancer.

Background: Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, and the median overall survival (OS) is approximately 2-3 years among patients with stage III disease. Furthermore, it is one of the deadliest types of cancer globally due to non-specific symptoms and the lack of a biomarker for early detection. The most important decision that clinicians need to make after a lung cancer diagnosis is the selection of a treatment schedule. This decision is based on, among others factors, the risk of developing metastasis. Methods: A cohort of 115 NSCLC patients treated using chemotherapy and radiotherapy (RT) with curative intent was retrospectively collated and included patients for whom positron emission tomography/computed tomography (PET/CT) images, acquired before RT, were available. The PET/CT images were used to compute radiomic features extracted from a region of interest (ROI), the primary tumor. Radiomic and clinical features were then classified to stratify the patients into short and long time to metastasis, and regression analysis was used to predict the risk of metastasis. Results: Classification based on binarized metastasis-free survival (MFS) was applied with moderate success. Indeed, an accuracy of 0.73 was obtained for the selection of features based on the Wilcoxon test and logistic regression model. However, the Cox regression model for metastasis risk prediction performed very well, with a concordance index (C-index) score equal to 0.84. Conclusions: It is possible to accurately predict the risk of metastasis in NSCLC patients based on radiomic features. The results demonstrate the potential use of features extracted from cancer imaging in predicting the risk of metastasis.

Mathematical modeling of regulatory networks of intracellular processes - Aims and selected methods.

Regulatory networks structure and signaling pathways dynamics are uncovered in time- and resource consuming experimental work. However, it is increasingly supported by modeling, analytical and computational techniques as well as discrete mathematics and artificial intelligence applied to to extract knowledge from existing databases. This review is focused on mathematical modeling used to analyze dynamics and robustness of these networks. This paper presents a review of selected modeling methods that facilitate advances in molecular biology.

Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation.

Immune cells fine tune their responses to infection and inflammatory cues. Here, using live-cell confocal microscopy and mathematical modelling, we investigate interferon-induced JAK-STAT signalling in innate immune macrophages. We demonstrate that transient exposure to IFN-γ stimulation induces a long-term desensitisation of STAT1 signalling and gene expression responses, revealing a dose- and time-dependent regulatory feedback that controls JAK-STAT responses upon re-exposure to stimulus. We show that IFN-α/ß1 elicit different level of desensitisation from IFN-γ, where cells refractory to IFN-α/ß1 are sensitive to IFN-γ, but not vice versa. We experimentally demonstrate that the underlying feedback mechanism involves regulation of STAT1 phosphorylation but is independent of new mRNA synthesis and cognate receptor expression. A new feedback model of the protein tyrosine phosphatase activity recapitulates experimental data and demonstrates JAK-STAT network's ability to decode relative changes of dose, timing, and type of temporal interferon stimulation. These findings reveal that STAT desensitisation renders cells with signalling memory of type I and II interferon stimulation, which in the future may improve administration of interferon therapy.

Application of Sensitivity Analysis to Discover Potential Molecular Drug Targets.

Mathematical modeling of signaling pathways and regulatory networks has been supporting experimental research for some time now. Sensitivity analysis, aimed at finding model parameters whose changes yield significantly altered cellular responses, is an important part of modeling work. However, sensitivity methods are often directly transplanted from analysis of technical systems, and thus, they may not serve the purposes of analysis of biological systems. This paper presents a novel sensitivity analysis method that is particularly suited to the task of searching for potential molecular drug targets in signaling pathways. Using two sample models of pathways, p53/Mdm2 regulatory module and IFN-ß-induced JAK/STAT signaling pathway, we show that the method leads to biologically relevant conclusions, identifying processes suitable for targeted pharmacological inhibition, represented by the reduction of kinetic parameter values. That, in turn, facilitates subsequent search for active drug components.

Petri nets and ODEs as complementary methods for comprehensive analysis on an example of the ATM-p53-NF-[Formula: see text]B signaling pathways.

Intracellular processes are cascades of biochemical reactions, triggered in response to various types of stimuli. Mathematical models describing their dynamics have become increasingly popular in recent years, as tools supporting experimental work in analysis of pathways and regulatory networks. Not only do they provide insights into general properties of these systems, but also help in specific tasks, such as search for drug molecular targets or treatment protocols. Different tools and methods are used to model complex biological systems. In this work, we focus on ordinary differential equations (ODEs) and Petri nets. We consider specific methods of analysis of such models, i.e., sensitivity analysis (SA) and significance analysis. So far, they have been applied separately, with different goals. In this paper, we show that they can complement each other, combining the sensitivity of ODE models and the significance analysis of Petri nets. The former is used to find parameters, whose change results in the greatest quantitative and qualitative changes in the model response, while the latter is a structural analysis and allows indicating the most important subprocesses in terms of information flow in Petri net. Ultimately, both methods facilitate finding the essential processes in a given signaling pathway or regulatory network and may be used to support medical therapy development. In the paper, the use of dual modeling is illustrated with an example of ATM/p53/NF-[Formula: see text]B pathway. Each method was applied to analyze this system, resulting in finding different subsets of important processes that might be prospective targets for changing this system behavior. While some of the processes were indicated in each of the approaches, others were found by one method only and would be missed if only that method was applied. This leads to the conclusion about the complementarity of the methods under investigation. The dual modeling approach of comprehensive structural and parametric analysis yields results that would not be possible if these two modeling approaches were applied separately. The combined approach, proposed in this paper, facilitates finding not only key processes, with which significant parameters are associated, but also significant modules, corresponding to subsystems of regulatory networks. The results provide broader insight into therapy targets in diseases in which the natural control of intracellular processes is disturbed, leading to the development of more effective therapies in medicine.

Heat shock response regulates stimulus-specificity and sensitivity of the pro-inflammatory NF-κB signalling.

BACKGROUND: Ability to adapt to temperature changes trough the Heat Shock Response (HSR) pathways is one of the most fundamental and clinically relevant cellular response systems. Heat Shock (HS) affects the signalling and gene expression responses of the Nuclear Factor κB (NF-κB) transcription factor, a critical regulator of proliferation and inflammation, however, our quantitative understanding of how cells sense and adapt to temperature changes is limited. METHODS: We used live-cell time-lapse microscopy and mathematical modelling to understand the signalling of the NF-κB system in the human MCF7 breast adenocarcinoma cells in response to pro-inflammatory Interleukin 1ß (IL1ß) and Tumour Necrosis Factor α (TNFα) cytokines, following exposure to a 37-43 °C range of physiological and clinical temperatures. RESULTS: We show that exposure to 43 °C 1 h HS inhibits the immediate NF-κB signalling response to TNFα and IL1ß stimulation although uptake of cytokines is not impaired. Within 4 h after HS treatment IL1ß-induced NF-κB responses return to normal levels, but the recovery of the TNFα-induced responses is still affected. Using siRNA knock-down of Heat Shock Factor 1 (HSF1) we show that this stimulus-specificity is conferred via the Inhibitory κB kinase (IKK) signalosome where HSF1-dependent feedback regulates TNFα, but not IL1ß-mediated IKK recovery post HS. Furthermore, we demonstrate that through the temperature-dependent denaturation and recovery of IKK, TNFα and IL1ß-mediated signalling exhibit different temperature sensitivity and adaptation to repeated HS when exposed to a 37-43 °C temperature range. Specifically, IL1ß-mediated NF-κB responses are more robust to temperature changes in comparison to those induced by TNFα treatment. CONCLUSIONS: We demonstrate that the kinetics of the NF-κB system following temperature stress is cytokine specific and exhibit differential adaptation to temperature changes. We propose that this differential temperature sensitivity is mediated via the IKK signalosome, which acts as a bona fide temperature sensor trough the HSR cross-talk. This novel quantitative understanding of NF-κB and HSR interactions is fundamentally important for the potential optimization of therapeutic hyperthermia protocols. Video Abstract.

LMO1 polymorphisms and the risk of neuroblastoma: Assessment of meta-analysis of case-control studies.

Neuroblastoma (NB), a neuroendocrine tumour, is one of the most prevalent cancers in children. The link between LMO1 polymorphisms and NB has been investigated by several groups, rendering inconclusive results. Here, with this comprehensive systematic review and up-to-date meta-analysis, we aim to distinctively elucidate the possible correlation between LMO1 polymorphisms and NB susceptibility. Eligible studies were systematically researched and identified using PubMed, Web of Science and Scopus databases up to 10 February 2019. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the strength of the associations. Our findings revealed that rs110419 and rs2168101 polymorphisms were significantly associated with a decreased risk of NB in all genetic models. In addition, the rs4758051 variant appeared protective against NB in homozygous, dominant and allele genetic models, whereas the rs10840002 variant markedly decreased the risk of NB in the allele model. In contrast, the rs204938 polymorphism showed a positive association with NB susceptibility in allele genetic models. In summary, our meta-analysis is the first to provide clear evidence of an association between specific polymorphisms of LMO1 and susceptibility to NB. Of note, additional larger well-designed studies would be helpful to further evaluate and confirm this association.

HBK-17, a 5-HT1A Receptor Ligand With Anxiolytic-Like Activity, Preferentially Activates ß-Arrestin Signaling.

Numerous studies have proven that both stimulation and blockade of 5-HT1A and the blockade of 5-HT7 receptors might cause the anxiolytic-like effects. Biased agonists selectively activate specific signaling pathways. Therefore, they might offer novel treatment strategies. In this study, we investigated the anxiolytic-like activity, as well as the possible mechanism of action of 1-[(2,5-dimethylphenoxy)propyl]-4-(2-methoxyphenyl)piperazine hydrochloride (HBK-17). In our previous experiments, HBK-17 showed high affinity for 5-HT1A and 5-HT7 receptors and antidepressant-like properties. We performed the four plate test and the elevated plus maze test to determine anxiolytic-like activity. Toward a better understanding of the pharmacological properties of HBK-17 we used various functional assays to determine its intrinsic activity at 5-HT1A, 5-HT2A, 5-HT7, and D2 receptors and UHPLC-MS/MS method to evaluate its pharmacokinetic profile. We observed the anxiolytic-like activity of HBK-17 in both behavioral tests and the effect was reversed by the pretreatment with WAY-100635, which proves that 5-HT1A receptor activation was essential for the anxiolytic-like effect. Moreover, the compound moderately antagonized D2, weakly 5-HT7 and very weakly 5-HT2A receptors. We demonstrated that HBK-17 preferentially activated ß-arrestin signaling after binding to the 5-HT1A receptor. HBK-17 was rapidly absorbed after intraperitoneal administration and had a half-life of about 150 min. HBK-17 slightly penetrated the peripheral compartment and showed bioavailability of approximately 45%. The unique pharmacological profile of HBK-17 encourages further experiments to understand its mechanism of action fully.

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level.

Elevated temperature induces the heat shock (HS) response, which modulates cell proliferation, apoptosis, the immune and inflammatory responses. However, specific mechanisms linking the HS response pathways to major cellular signaling systems are not fully understood. Here we used integrated computational and experimental approaches to quantitatively analyze the crosstalk mechanisms between the HS-response and a master regulator of inflammation, cell proliferation, and apoptosis the Nuclear Factor κB (NF-κB) system. We found that populations of human osteosarcoma cells, exposed to a clinically relevant 43°C HS had an attenuated NF-κB p65 response to Tumor Necrosis Factor α (TNFα) treatment. The degree of inhibition of the NF-κB response depended on the HS exposure time. Mathematical modeling of single cells indicated that individual crosstalk mechanisms differentially encode HS-mediated NF-κB responses while being consistent with the observed population-level responses. In particular "all-or-nothing" encoding mechanisms were involved in the HS-dependent regulation of the IKK activity and IκBα phosphorylation, while others involving transport were "analogue". In order to discriminate between these mechanisms, we used live-cell imaging of nuclear translocations of the NF-κB p65 subunit. The single cell responses exhibited "all-or-nothing" encoding. While most cells did not respond to TNFα stimulation after a 60 min HS, 27% showed responses similar to those not receiving HS. We further demonstrated experimentally and theoretically that the predicted inhibition of IKK activity was consistent with the observed HS-dependent depletion of the IKKα and IKKß subunits in whole cell lysates. However, a combination of "all-or-nothing" crosstalk mechanisms was required to completely recapitulate the single cell data. We postulate therefore that the heterogeneity of the single cell responses might be explained by the cell-intrinsic variability of HS-modulated IKK signaling. In summary, we show that high temperature modulates NF-κB responses in single cells in a complex and unintuitive manner, which needs to be considered in hyperthermia-based treatment strategies.

Sensitivity of signaling pathway dynamics to plasmid transfection and its consequences.

This paper deals with development of signaling pathways models and using plasmid-based experiments to support parameter estimation. We show that if cells transfected with plasmids are used in experiments, the models should include additional components that describe explicitly effects induced by plasmids. Otherwise, when the model is used to analyze responses of wild type, i.e. non-transfected cells, it may not capture their dynamics properly or even lead to false conclusions. In order to illustrate this, an original mathematical model of miRNA-mediated control of gene expression in the NFκB pathway is presented. The paper shows what artifacts might appear due to experimental procedures and how to develop the models in order to avoid pursuing these artifacts instead of real kinetics.

Chemically Homogenous Compounds with Antagonistic Properties at All α1-Adrenoceptor Subtypes but not ß1-Adrenoceptor Attenuate Adrenaline-Induced Arrhythmia in Rats.

Studies proved that among all α1-adrenoceptors, cardiac myocytes functionally express only α1A- and α1B-subtype. Scientists indicated that α1A-subtype blockade might be beneficial in restoring normal heart rhythm. Therefore, we aimed to determine the role of α1-adrenoceptors subtypes (i.e., α1A and α1B) in antiarrhythmic effect of six structurally similar derivatives of 2-methoxyphenylpiperazine. We compared the activity of studied compounds with carvedilol, which is ß1- and α1-adrenoceptors blocker with antioxidant properties. To evaluate the affinity for adrenergic receptors, we used radioligand methods. We investigated selectivity at α1-adrenoceptors subtypes using functional bioassays. We tested antiarrhythmic activity in adrenaline-induced (20 µg/kg i.v.), calcium chloride-induced (140 and 25 mg/kg i.v.) and barium chloride-induced (32 and 10 mg/kg i.v.) arrhythmia models in rats. We also evaluated the influence of studied compounds on blood pressure in rats, as well as lipid peroxidation. All studied compounds showed high affinity toward α1-adrenoceptors but no affinity for ß1 receptors. Biofunctional studies revealed that the tested compounds blocked α1A-stronger than α1B-adrenoceptors, but except for HBK-19 they antagonized α1A-adrenoceptor weaker than α1D-subtype. HBK-19 showed the greatest difference in pA2 values-it blocked α1A-adrenoceptors around seven-fold stronger than α1B subtype. All compounds showed prophylactic antiarrhythmic properties in adrenaline-induced arrhythmia, but only the activity of HBK-16, HBK-17, HBK-18, and HBK-19 (ED50 = 0.18-0.21) was comparable to that of carvedilol (ED50 = 0.36). All compounds reduced mortality in adrenaline-induced arrhythmia. HBK-16, HBK-17, HBK-18, and HBK-19 showed therapeutic antiarrhythmic properties in adrenaline-induced arrhythmia. None of the compounds showed activity in calcium chloride- or barium chloride-induced arrhythmias. HBK-16, HBK-17, HBK-18, and HBK-19 decreased heart rhythm at ED84. All compounds significantly lowered blood pressure in normotensive rats. HBK-18 showed the strongest hypotensive properties (the lowest active dose: 0.01 mg/kg). HBK-19 was the only compound in the group, which did not show hypotensive effect at antiarrhythmic doses. HBK-16, HBK-17, HBK-18, HBK-19 showed weak antioxidant properties. Our results indicate that the studied 2-methoxyphenylpiperazine derivatives that possessed stronger α1A-adrenolytic properties (i.e., HBK-16, HBK-17, HBK-18, and HBK-19) were the most active compounds in adrenaline-induced arrhythmia. Thus, we suggest that the potent blockade of α1A-receptor subtype is essential to attenuate adrenaline-induced arrhythmia.

Modeling epigenetic regulation of PRC1 protein accumulation in the cell cycle.

BACKGROUND: Epigenetic regulation contributes to many important processes in biological cells. Examples include developmental processes, differentiation and maturation of stem cells, evolution of malignancy and other. Cell cycle regulation has been subject of mathematical modeling by a number of authors that resulted in many interesting models and application of analytic techniques ranging from stochastic processes to partial differential equations and to integral, functional and operator equations. In this paper we address the question of how the regulation of protein contents influences the long-term dynamics of the population. To accomplish this, we follow the philosophy of a 1984 model by Kimmel et al., but adjust the details to fit the experimental data on protein PRC1 from a more recent paper. RESULTS: We built a model of cell cycle dynamics of the PRC1 and fitted it to the data made available by Cohen and his co-authors. We have run the model for a large number of cell generations, recording the PRC1 contents in all cells of the resulting pedigree, at constant time intervals. During cell division the PRC1 is unequally divided between daughter cells. The picture emerging from simulations of Data set 1 is that of a very well-tuned regulatory circuit that provides a stable distribution of PRC1 contents and interdivision times. Data set 2 seems qualitatively different, with more variation in cell cycle duration. CONCLUSIONS: The main question we address is whether the regulatory feedbacks deduced from single cell cycle data provide epigenetic regulation of cell characteristics in long run. PRC1 is a good candidate because of its role in setting timing of division. Findings of the current paper include tight regulation of the cell cycle (particularly the timing of the cell cycle) even that PRC1 is only one of the players in cell dynamics. Understanding that association, even close, does not necessarily imply causation, we consider this an interesting and important result.

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.

Model-based analysis of interferon-beta induced signaling pathway.

MOTIVATION: Interferon-beta induced JAK-STAT signaling pathways contribute to mucosal immune recognition and an anti-viral state. Though the main molecular mechanisms constituting these pathways are known, neither the detailed structure of the regulatory network, nor its dynamics has yet been investigated. The objective of this work is to build a mathematical model for the pathway that would serve two purposes: (1) to reproduce experimental results in simulation of both early and late response to Interferon-beta stimulation and (2) to explain experimental phenomena generating new hypotheses about regulatory mechanisms that cannot yet be tested experimentally. RESULTS: Experimentally determined time dependent changes in the major components of this pathway were used to build a mathematical model describing pathway dynamics in the form of ordinary differential equations. The experimental results suggested existence of unknown negative control mechanisms that were tested numerically using the model. Together, experimental and numerical data show that the epithelial JAK-STAT pathway might be subjected to previously unknown dynamic negative control mechanisms: (1) activation of dormant phosphatases and (2) inhibition of nuclear import of IRF1.

Analysis and optimization of drug resistant and phase-specific cancer chemotherapy models.

This paper presents analysis and biomedical implications of a certain class of bilinear systems that can be applied in modeling of cancer chemotherapy. It combines models that so far have been studied separately, taking into account both the phenomenon of gene amplification and drug specificity in chemotherapy in their different aspects. The methodology of analysis of such models, based on system decomposition, is discussed. The mathematical description is given by an infinite dimensional state equation with a system matrix, the form of which allows decomposing the model into two interacting subsystems. While the first one, of a finite dimension, can have any form, the second one is infinite-dimensional and tridiagonal. Then the optimal control problem is defined in l1 space. To derive necessary conditions for optimal control, the model description is transformed into an integrodifferential one.