Charting the NF-kB pathway interactome map

One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as “inflammaging”, negatively correlated with longevity. The five components of the Nuclear Factor kB (NF-kB) family are prominent mediators of inflammation. Several different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of this analysis is to provide a wider, systemic picture of such intricate signaling system

Charting the NF-κB Pathway Interactome Map

Inflammation is part of a complex physiological response to harmful stimuli and pathogenic stress. The five components of the Nuclear Factor κB (NF-κB) family are prominent mediators of inflammation, acting as key transcriptional regulators of hundreds of genes. Several signaling pathways activated by diverse stimuli converge on NF-κB activation, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of the present analysis is to provide a wider, systemic picture of the NF-κB signaling system. Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct a single, comprehensive picture of the proteins that interact with, and participate to the NF-κB activation system. Such a reconstruction shows that the NF-κB interactome is substantially different in quantity and quality of components with respect to canonical representations. The analysis highlights that several neglected but topologically central proteins may play a role in the activation of NF-κB mediated responses. Moreover the interactome structure fits with the characteristics of a bow tie architecture. This interactome is intended as an open network resource available for further development, refinement and analysis

A novel combined scientific and artistic approach for the advanced characterization of interactomes: The akirin/subolesin model

The main objective of this study was to propose a novel methodology to approach challenges in molecular biology. Akirin/Subolesin (AKR/SUB) are vaccine protective antigens and are a model for the study of the interactome due to its conserved function in the regulation of different biological processes such as immunity and development throughout the metazoan. Herein, three visual artists and a music professor collaborated with scientists for the functional characterization of the AKR2 interactome in the regulation of the NF-¿B pathway in human placenta cells. The results served as a methodological proof-of-concept to advance this research area. The results showed new perspectives on unexplored characteristics of AKR2 with functional implications. These results included protein dimerization, the physical interactions with different proteins simultaneously to regulate various biological processes defined by cell type-specific AKR– protein interactions, and how these interactions positively or negatively regulate the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-¿B) signaling pathway in a biological context-dependent manner. These results suggested that AKR2-interacting proteins might constitute suitable secondary transcription factors for cell-and stimulus-specific regulation of NF-¿B. Musical perspective supported AKR/SUB evolutionary conservation in different species and provided new mechanistic insights into the AKR2 interactome. The combined scientific and artistic perspectives resulted in a multidisciplinary approach, advancing our knowledge on AKR/SUB interactome, and provided new insights into the function of AKR2–protein interactions in the regulation of the NF-¿B pathway. Additionally, herein we proposed an algorithm for quantum vaccinomics by focusing on the model proteins AKR/SUB. © 2020 by the authors. Licensee MDPI, Basel, Switzerland

On chaotic dynamics in transcription factors and the associated effects in differential gene regulation

It is becoming clear that the dynamics of transcription factors may be important for gene regulation. Here, the authors study the implications of oscillatory and chaotic dynamics of NF-κB and demonstrate that it allows a degree of control of gene expression and can generate phenotypic heterogeneity

Developmental dynamics of transcription and genome architecture

Abstract Regulation of gene expression is necessary for the control of complex developmental processes. The genome has to shape in specific conformations to fit inside the nucleus and to tether specific regulatory elements to their target genes. Although the linear composition of many genomes is largely known, their three dimensional (3D) organization and dynamics are largely unknown. Hence, in order to unravel gene regulation, it is necessary to understand the chromatin structure and organization. Furthermore, developmental procedures are controlled by complex combinatorial transcription factor (TF) networks. Hence, unveiling those networks will provide a better insight towards understanding those developmental procedures. The work described in this thesis aims to study the genome conformation/interactome and their effect on gene regulation and to unveil the role of transcription factor proteins (TFs) in complex developmental processes

Functional/Activity Network (FAN) Analysis of Gene-Phenotype Connectivity Liaised by Grape Polyphenol Resveratrol

Resveratrol is a polyphenol that has witnessed an unprecedented yearly growth in PubMed citations since the late 1990s. Based on the diversity of cellular processes and diseases resveratrol reportedly affects and benefits, it is likely that the interest in resveratrol will continue, although uncertainty regarding its mechanism in different biological systems remains.We hypothesize that insights on disease-modulatory activities of resveratrol might be gleaned by systematically dissecting the publicly available published data on chemicals and drugs. In this study, we tested our hypothesis by querying DTome (Drug-Target Interactome), a web-based tool containing data compiled from open-source databases including DrugBank, PharmGSK, and Protein Interaction Network Analysis (PINA). Four direct protein targets (DPT) and 219 DPT-associated genes were identified for resveratrol. The DPT-associated genes were scrutinized by WebGestalt (WEB-based Gene SeT Analysis Toolkit). This enrichment analysis resulted in 10 identified KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Refined analysis of KEGG pathways showed that 2 - one linked to p53 and a second to prostate cancer - have functional connectivity to resveratrol and its four direct protein targets. These results suggest that a functional activity network (FAN) approach may be considered as a new paradigm for guiding future studies of resveratrol. FAN analysis resembles a BioGPS, with capability for mapping a Web-based scientific track that can productively and cost effectively connect resveratrol to its primary and secondary target proteins and to its biological functions

Identification and characterization of the role played by the neuronal NCX2 in glioblastoma progression and malignity

Glioblastoma multiforme (GBM) is one of the most malignant primary brain tumors with an aggressive phenotype and poor lines of evidence in genetic or environmental risk factors. In addition, glioblastoma patients show an ineffective treatment and a very short survival rate. For these reasons, there is a great demand of novel pharmacological targets for new effective strategies of treatment. A common feature of all GBM sub-types is the alteration in the activity of pathways controlling the expression of several transcription factors involved in the up- or down-regulation of pro-oncogenes or anti-oncogenes, respectively. Among the downregulated genes there is Slc8a2 encoding for the brain Sodium Calcium Exchanger 2 (NCX2). Recent data suggest that this antiporter can represent a possible anti-oncogene for GBM since it is silenced in all glioma stages. To explore the genetic and epigenetic mechanisms leading to NCX2 downregulation, we identified, cloned and analyzed both rat and human slc8a2 promoters in two cell lines PC12 and U87 expressing high or low level of this antiporter, respectively. In addition, we selected several transcription factors (TFs) able to modify both rat and human promoter activity of NCX2 in PC12 and U87 cell lines. However, TFs were able to increase mRNA expression of endogenous NCX2 only in PC12 cells. Interestingly, pharmacological inhibition of EGF pathway at different points restored NCX2 mRNA expression levels and increased its promoter activity in U87 cells. Moreover, transfection of NFkB, a downstream transcription factor of EGF pathway, downregulated NCX2 expression even in the presence of an inhibitor of EGF pathway. In addition, the blockage of this receptor-dependent cascade, or the stably transfection of NCX2, or the other isoform NCX1, hampered cell growth of U87 cells. In a prospective therapeutic approach, we also analyzed the effect of two compounds, namely neurounina-1 and CN-PYB2, on the vitality and cell growth of U87 cell line. Neurounina-1 is a stimulator of both NCX1 and NCX2 activity, whereas CN-PYB2 is a selective stimulator of NCX1 activity. Results showed that these compounds hampered in a concentration- and time-dependent manner cell growth of U87 cell line, whereas they were ineffective in other cell lines, including BHK, SH-SH5Y and PC12. Altogether, these data suggest that glioblastoma silences NCX2 by an EGF pathway via NFkB, and the increase of NCX expression via EGF-pathway inhibition, or the increase of NCX activity, slows-down glioblastoma cell growth and thus might exert a tumor suppressor effect