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Abstract Background Triple negative breast cancer (TNBC) is the most aggressive subtype of breast cancer (BC). Treatment options for TNBC patients are limited and further insights into disease aetiology are needed to develop better therapeutic approaches. microRNAs’ ability to regulate multiple targets could hold a promising discovery approach to pathways relevant for TNBC aggressiveness. Thus, we address the role of miRNAs in controlling three signalling pathways relevant to the biology of TNBC, and their downstream phenotypes. Methods To identify miRNAs regulating WNT/β-catenin, c-Met, and integrin signalling pathways, we performed a high-throughput targeted proteomic approach, investigating the effect of 800 miRNAs on the expression of 62 proteins in the MDA-MB-231 TNBC cell line. We then developed a novel network analysis, Pathway Coregulatory (PC) score, to detect miRNAs regulating these three pathways. Using in vitro assays for cell growth, migration, apoptosis, and stem-cell content, we validated the function of candidate miRNAs. Bioinformatic analyses using BC patients’ datasets were employed to assess expression of miRNAs as well as their pathological relevance in TNBC patients. Results We identified six candidate miRNAs coordinately regulating the three signalling pathways. Quantifying cell growth of three TNBC cell lines upon miRNA gain-of-function experiments, we characterised miR-193b as a strong and consistent repressor of proliferation. Importantly, the effects of miR-193b were stronger than chemical inhibition of the individual pathways. We further demonstrated that miR-193b induced apoptosis, repressed migration, and regulated stem-cell markers in MDA-MB-231 cells. Furthermore, miR-193b expression was the lowest in patients classified as TNBC or Basal compared to other subtypes. Gene Set Enrichment Analysis showed that miR-193b expression was significantly associated with reduced activity of WNT/β-catenin and c-Met signalling pathways in TNBC patients. Conclusions Integrating miRNA-mediated effects and protein functions on networks, we show that miRNAs predominantly act in a coordinated fashion to activate or repress connected signalling pathways responsible for metastatic traits in TNBC. We further demonstrate that our top candidate, miR-193b, regulates these phenotypes to an extent stronger than individual pathway inhibition, thus emphasizing that its effect on TNBC aggressiveness is mediated by the coordinated repression of these functionally interconnected pathways.

Abstract Background Stroke can lead to cardiac dysfunction in patients, but the mechanisms underlying the interaction between the injured brain and the heart are poorly understood. The objective of the study is to investigate the effects of experimental murine stroke on cardiac function and molecular signalling in the heart. Methods and results Mice were subjected to filament‐induced left middle cerebral artery occlusion for 30 or 60 min or sham surgery and underwent repetitive micro‐echocardiography. Left ventricular contractility was reduced early (24–72 h) but not late (2 months) after brain ischaemia. Cardiac dysfunction was accompanied by a release of high‐sensitive cardiac troponin (hsTNT (ng/ml): d1: 7.0 ± 1.0 vs. 25.0 ± 3.2*; d3: 7.3 ± 1.1 vs. 52.2 ± 16.7*; d14: 5.7 ± 0.8 vs. 5.2 ± 0.3; sham vs. 60 min. MCAO; mean ± SEM; *p

In recent years, the interest in semi-supervised learning has increased, combining supervised and unsupervised learning approaches. This is especially valid for classification applications in remote sensing, while the data acquisition rate in current systems has become fairly large considering high- and very-high resolution data; yet on the other hand, the process of obtaining the ground truth data may be cumbersome for such large repositories. In this paper, we investigate the application of semi-supervised learning approaches and particularly focus on the small sample size problem. To that extend, we consider two basic unsupervised approaches by enlarging the initial labeled training set as well as an ensemble-based self-training method. We propose different strategies within self-training on how to select more reliable candidates from the pool of unlabeled samples to speed-up the learning process and to improve the classification performance of the underlying classifier ensemble. We evaluate the effectiveness of the proposed semi-supervised learning approach over polarimetric SAR data. Results show that the proposed self-training approach using an ensemble-based classifier that is initially trained over a small training set can achieve a similar performance level of a fully supervised learning approach where the training is performed over significantly larger labeled data. Considering the difficulties of the manual data labeling in such massive volumes of SAR repositories, this is indeed a promising accomplishment for semi-supervised SAR classification.

Abstract The EGFR‐driven cell‐cycle pathway has been extensively studied due to its pivotal role in breast cancer proliferation and pathogenesis. Although several studies reported regulation of individual pathway components by microRNAs (miRNAs), little is known about how miRNAs coordinate the EGFR protein network on a global miRNA (miRNome) level. Here, we combined a large‐scale miRNA screening approach with a high‐throughput proteomic readout and network‐based data analysis to identify which miRNAs are involved, and to uncover potential regulatory patterns. Our results indicated that the regulation of proteins by miRNAs is dominated by the nucleotide matching mechanism between seed sequences of the miRNAs and 3′‐UTR of target genes. Furthermore, the novel network‐analysis methodology we developed implied the existence of consistent intrinsic regulatory patterns where miRNAs simultaneously co‐regulate several proteins acting in the same functional module. Finally, our approach led us to identify and validate three miRNAs (miR‐124, miR‐147 and miR‐193a‐3p) as novel tumor suppressors that co‐target EGFR‐driven cell‐cycle network proteins and inhibit cell‐cycle progression and proliferation in breast cancer.

Recent development of high-throughput, multiplexing technology has initiated projects that systematically investigate interactions between two types of components in biological networks, for instance transcription factors and promoter sequences, or microRNAs (miRNAs) and mRNAs. In terms of network biology, such screening approaches primarily attempt to elucidate relations between biological components of two distinct types, which can be represented as edges between nodes in a bipartite graph. However, it is often desirable not only to determine regulatory relationships between nodes of different types, but also to understand the connection patterns of nodes of the same type. Especially interesting is the co-occurrence of two nodes of the same type, i.e., the number of their common neighbours, which current high-throughput screening analysis fails to address. The co-occurrence gives the number of circumstances under which both of the biological components are influenced in the same way. Here we present SICORE, a novel network-based method to detect pairs of nodes with a statistically significant co-occurrence. We first show the stability of the proposed method on artificial data sets: when randomly adding and deleting observations we obtain reliable results even with noise exceeding the expected level in large-scale experiments. Subsequently, we illustrate the viability of the method based on the analysis of a proteomic screening data set to reveal regulatory patterns of human microRNAs targeting proteins in the EGFR-driven cell cycle signalling system. Since statistically significant co-occurrence may indicate functional synergy and the mechanisms underlying canalization, and thus hold promise in drug target identification and therapeutic development, we provide a platform-independent implementation of SICORE with a graphical user interface as a novel tool in the arsenal of high-throughput screening analysis.

Color is the major source of information widely used in image analysis and content-based retrieval. Extracting dominant colors that are prominent in a visual scenery is of utmost importance since the human visual system primarily uses them for perception and similarity judgment. In this paper, we address dominant color extraction as a dynamic clustering problem and use techniques based on Particle Swarm Optimization (PSO) for finding optimal (number of) dominant colors in a given color space, distance metric and a proper validity index function. The first technique, so-called Multidimensional (MD) PSO can seek both positional and dimensional optima. Nevertheless, MD PSO is still susceptible to premature convergence due to lack of divergence. To address this problem we then apply Fractional Global Best Formation (FGBF) technique. In order to extract perceptually important colors and to further improve the discrimination factor for a better clustering performance, an efficient color distance metric, which uses a fuzzy model for computing color (dis-) similarities over HSV (or HSL) color space is proposed. The comparative evaluations against MPEG-7 dominant color descriptor show the superiority of the proposed technique.