Linking proteins to signaling pathways for experiment design and evaluation

Biomedical experimental work often focuses on altering the functions of selected proteins. These changes can hit signaling pathways, and can therefore unexpectedly and non-specifically affect cellular processes. We propose PathwayLinker, an online tool that can provide a first estimate of the possible signaling effects of such changes, e.g., drug or microRNA treatments. PathwayLinker minimizes the users' efforts by integrating protein-protein interaction and signaling pathway data from several sources with statistical significance tests and clear visualization. We demonstrate through three case studies that the developed tool can point out unexpected signaling bias in normal laboratory experiments and identify likely novel signaling proteins among the interactors of known drug targets. In our first case study we show that knockdown of the Caenorhabditis elegans gene cdc-25.1 (meant to avoid progeny) may globally affect the signaling system and unexpectedly bias experiments. In the second case study we evaluate the loss-of-function phenotypes of a less known C. elegans gene to predict its function. In the third case study we analyze GJA1, an anti-cancer drug target protein in human, and predict for this protein novel signaling pathway memberships, which may be sources of side effects. Compared to similar services, a major advantage of PathwayLinker is that it drastically reduces the necessary amount of manual literature searches and can be used without a computational background. PathwayLinker is available at http://PathwayLinker.org. Detailed documentation and source code are available at the website. © 2012 Farkas et al

Intracellular and intercellular signaling networks in cancer initiation, development and precision anti-cancer therapy: RAS acts as contextual signaling hub

Cancer initiation and development are increasingly perceived as systems-level phenomena, where intra- and inter-cellular signaling networks of the ecosystem of cancer and stromal cells offer efficient methodologies for outcome prediction and intervention design. Within this framework, RAS emerges as a ‘contextual signaling hub’, i.e. the final result of RAS activation or inhibition is determined by the signaling network context. Current therapies often ‘train’ cancer cells shifting them to a novel attractor, which has increased metastatic potential and drug resistance. The few therapy-surviving cancer cells are surrounded by massive cell death triggering a primordial adaptive and reparative general wound healing response. Overall, dynamic analysis of patient- and disease-stage specific intracellular and intercellular signaling networks may open new areas of anticancer therapy using multitarget drugs, drugs combinations, edgetic drugs, as well as help design ‘gentler’, differentiation and maintenance therapies. © 2016 Elsevier Lt

TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species

Analysis of transcriptional regulatory interactions and their comparisons across multiple species are crucial for progress in various fields in biology, from functional genomics to the evolution of signal transduction pathways. However, despite the rapidly growing body of data on regulatory interactions in several eukaryotes, no databases exist to provide curated high-quality information on transcription factor-target gene interactions for multiple species. Here, we address this gap by introducing the TFLink gateway, which uniquely provides experimentally explored and highly accurate information on transcription factor-target gene interactions (∼12 million), nucleotide sequences and genomic locations of transcription factor binding sites (∼9 million) for human and six model organisms: mouse, rat, zebrafish, fruit fly, worm and yeast by integrating 10 resources. TFLink provides user-friendly access to data on transcription factor-target gene interactions, interactive network visualizations and transcription factor binding sites, with cross-links to several other databases. Besides containing accurate information on transcription factors, with a clear labelling of the type/volume of the experiments (small-scale or high-throughput), the source database and the original publications, TFLink also provides a wealth of standardized regulatory data available for download in multiple formats. The database offers easy access to high-quality data for wet-lab researchers, supplies data for gene set enrichment analyses and facilitates systems biology and comparative gene regulation studies. Database URL https://tflink.net/

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches

The epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn's disease or ulcerative colitis

Linking Proteins to Signaling Pathways for Experiment Design and Evaluation

Biomedical experimental work often focuses on altering the functions of selected proteins. These changes can hit signaling pathways, and can therefore unexpectedly and non-specifically affect cellular processes. We propose PathwayLinker, an online tool that can provide a first estimate of the possible signaling effects of such changes, e.g., drug or microRNA treatments. PathwayLinker minimizes the users' efforts by integrating protein-protein interaction and signaling pathway data from several sources with statistical significance tests and clear visualization. We demonstrate through three case studies that the developed tool can point out unexpected signaling bias in normal laboratory experiments and identify likely novel signaling proteins among the interactors of known drug targets. In our first case study we show that knockdown of the Caenorhabditis elegans gene cdc-25.1 (meant to avoid progeny) may globally affect the signaling system and unexpectedly bias experiments. In the second case study we evaluate the loss-of-function phenotypes of a less known C. elegans gene to predict its function. In the third case study we analyze GJA1, an anti-cancer drug target protein in human, and predict for this protein novel signaling pathway memberships, which may be sources of side effects. Compared to similar services, a major advantage of PathwayLinker is that it drastically reduces the necessary amount of manual literature searches and can be used without a computational background. PathwayLinker is available at http://PathwayLinker.org. Detailed documentation and source code are available at the website

A global view of drug-therapy interactions

Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6), transportation infrastructures (7) and social communities (8,9) to biological systems (1,10,11). Even though new highthroughput technologies have rapidly been generating large amounts of genomic data, drug design has not followed the same development, and it is still complicated and expensive to develop new single-target drugs. Nevertheless, recent approaches suggest that multi-target drug design combined with a network-dependent approach and large-scale systems-oriented strategies (12-14) create a promising framework to combat complex multigenetic disorders like cancer or diabetes. Here, we investigate the human network corresponding to the interactions between all US approved drugs and human therapies, defined by known drug-therapy relationships. Our results show that the key paths in this network are shorter than three steps, indicating that distant therapies are separated by a surprisingly low number of chemical compounds. We also identify a sub-network composed by drugs with high centrality measures (15), which represent the structural back-bone of the drug-therapy system and act as hubs routing information between distant parts of the network. These findings provide for the first time a global map of the largescale organization of all known drugs and associated therapies, bringing new insights on possible strategies for future drug development. Special attention should be given to drugs which combine the two properties of (a) having a high centrality value and (b) acting on multiple targets.Comment: 16 pages, 4 figures. It was submitted to peer review on August 15, 200

SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation

Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. Salmonella serovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of gastro-intestinal strains than to each other indicating a parallel evolution of this trait. Given the complexity of the differences, a systems-level comparison could reveal key mechanisms enabling extra-intestinal serovars to cause systemic infections. Accordingly, in this work, we introduce a unique resource, SalmoNet, which combines manual curation, high-throughput data and computational predictions to provide an integrated network for Salmonella at the metabolic, transcriptional regulatory and protein-protein interaction levels. SalmoNet provides the networks separately for five gastro-intestinal and five extra-intestinal strains. As a multi-layered, multi-strain database containing experimental data, SalmoNet is the first dedicated network resource for Salmonella. It comprehensively contains interactions between proteins encoded in Salmonella pathogenicity islands, as well as regulatory mechanisms of metabolic processes with the option to zoom-in and analyze the interactions at specific loci in more detail. Application of SalmoNet is not limited to strain comparisons as it also provides a Salmonella resource for biochemical network modeling, host-pathogen interaction studies, drug discovery, experimental validation of novel interactions, uncovering new pathological mechanisms from emergent properties and epidemiological studies. SalmoNet is available at http://salmonet.org

Identification of critical paralog groups with indispensable roles in the regulation of signaling flow

Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in human signaling networks, we developed a signaling network-based method using cross-talk annotation and tissue-specific signaling flow analysis. 75 CPGs were found with higher degree, betweenness centrality, closeness, and ‘bowtieness’ when compared to other paralogs or other proteins in the signaling network. CPGs had higher diversity in all these measures, with more varied biological functions and more specific post-transcriptional regulation than non-critical paralog groups (non-CPG). Using TGF-beta, Notch and MAPK pathways as examples, SMAD2/3, NOTCH1/2/3 and MEK3/6-p38 CPGs were found to regulate the signaling flow of their respective pathways. Additionally, CPGs showed a higher mutation rate in both inherited diseases and cancer, and were enriched in drug targets. In conclusion, the results revealed two distinct types of paralog groups in the signaling network: CPGs and non-CPGs. Thus highlighting the importance of CPGs as compared to non-CPGs in drug discovery and disease pathogenesis

Взаємозв’язок між маркетинговою стратегією футбольного клубу та поведінкою споживачів різних вікових груп: досвід Словаччини

Ця стаття узагальнює аргументи та контраргументи в межах наукової дискусії з питання формування маркетингової стратегії компанії. Зазначено, що маркетингове дослідження являється інформаційною основою корпоративної стратегії, тоді як розробка маркетингової стратегії ґрунтується на цілях корпоративної стратегії. При цьому незважаючи на актуальність спортивних заходів у Словаччині, проведення яких розпочалося з початку ХХ століття, теперішній рівень розвитку спортивної галузі не відповідає сучасним показникам економічного розвитку. У свою чергу, країни Західної Європи досягли вищого рівня розвитку раніше, ніж пострадянські країни завдяки кращому рівню економічного розвитку. У свою чергу, у статті зазначено, що політичні та економічні зміни 90-х років ХХ століття та розширення ЄС відкрили нове вікно економічних можливостей для Словаччини. Таким чином, маркетинг спорту досяг відповідного прогресу; відбулася заміна застарілих спортивних споруд сучасними та добре обладнаними приміщеннями; клієнти отримали широкий асортимент спортивного обладнання та послуг. Головною метою даної статті є аналіз послуг та продуктів футбольного клубу Словацької Прем’єр-ліги (Fortuna League) з точки зору споживання, а також узагальнення досвіду та відгуків клієнтів акцентуючись на аспектах маркетингу. У рамках даного дослідження сформовано дві гіпотези. Для перевірки сформованих гіпотез використано критерій незалежності хі-квадрат, за допомогою якого досліджено декілька змінних одночасно та їх спільний розподіл. Враховуючи отримані результати, автори відмітили значний зв’язок між віковими групами та споживчою поведінкою на футбольних матчах. Більше того, отримані результати свідчать про те, що вік та відстань від місця проведення спортивного заходу не впливають на відвідування заходу фанатами футбольного клубу. Результати дослідження мають практичне значення і можуть бути прийняті до впровадження футбольними клубами Словаччини для удосконалення та підвищення ефективності маркетингової діяльності.The basis of modern company management is the marketing concept, the customer-oriented management and strategic planning, the managerial decisions matching the market opportunities, challenges and the company objectives and opportunities. The marketing research is the input for corporate strategy, while on the other hand elaboration of the marketing strategy is based on the objectives of corporate strategy. The sports developments that started at the beginning of the 20th.century have been of high relevance, but still incomparable to the current measure of development. Generally, the countries of Western-Europe, due to their better economic performance, have achieved a higher level of development far earlier than the post-communist countries. The political and economic change of the 90s in the 20th century, later the EU enlargement opened a range of new economic opportunities also for our region. The sports marketing, similarly to marketing activity in other sectors and fields, has made relevant progress. The obsolete sports facilities were replaced by modern and well-equipped facilities. The customers were offered a wide variety of sports equipment and sports services. The objective of the research is to examine the services and products of a football club in the Slovak Premier League (Fortuna League) in terms of consumerism, as well as to summarize the consumer experience and opinion, emphasizing the marketing aspect. We formulated two hypotheses in this study. Chi-square test of independence was used for testing our hypotheses, by the help of which we examined several variables at the same time – and also the joint distribution of several variables. The results show a significant relationship between the age groups and the consumer habit of the customers at football matches. The outcome of the study also indicates that neither the age nor the distance from the sports event can influence the fans of the football club to attend the sporting event. Our results could be used by Slovak football clubs to make their marketing more precise and more efficient

Oncogenic KRAS signaling and YAP1/β-catenin: Similar cell cycle control in tumor initiation

>Why are YAP1 and c-Myc often overexpressed (or activated) in KRAS-driven cancers and drug resistance? Here, we propose that there are two independent pathways in tumor proliferation: one includes MAPK/ERK and PI3K/A kt/mTOR; and the other consists of pathways leading to the expression (or activation) of YAP1 and c-Myc. KRAS contributes through the first. MYC is regulated by e.g. β-catenin, Notch and Hedgehog. We propose that YAP1 and ERK accomplish similar roles in cell cycle control, as do β-catenin and PI3K. This point is compelling, since the question of how YAP1 rescues K-Ras or B-Raf ablation has recently captured much attention, as well as the mechanism of resistance to PI3K inhibitors. The similarity in cell cycle actions of β-catenin and PI3K can also clarify the increased aggressiveness of lung cancer when both K-Ras and β-catenin operate. >Thus, we propose that the two pathways can substitute one another – or together amplify each other – in promoting proliferation. This new understanding of the independence and correspondence of the two pathways in cancer – MAPK/ERK and PI3K/Akt/mTOR; and YAP1 and c-Myc – provide a coherent and significant picture of signaling-driven oncogenic proliferation and may help in judicious, pathway-based drug discovery. © 2016 Ruth Nussino