ABSTRACT
SUMMARY: Literature exploration in PubMed on a large number of biomedical entities (e.g. genes, diseases or experiments) can be time-consuming and challenging, especially when assessing associations between entities. Here, we describe SimText, a user-friendly toolset that provides customizable and systematic workflows for the analysis of similarities among a set of entities based on text. SimText can be used for (i) text collection from PubMed and extraction of words with different text mining approaches, and (ii) interactive analysis and visualization of data using unsupervised learning techniques in an interactive app. AVAILABILITY AND IMPLEMENTATION: We developed SimText as an open-source R software and integrated it into Galaxy (https://usegalaxy.eu), an online data analysis platform with supporting self-learning training material available at https://training.galaxyproject.org. A command-line version of the toolset is available for download from GitHub (https://github.com/dlal-group/simtext) or as Docker image (https://hub.docker.com/r/dlalgroup/simtext/tags.). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Subject(s)
Data Mining , Software , Data Mining/methods , PubMed , Data Interpretation, Statistical , Data AnalysisABSTRACT
RATIONALE: Kv1.5 (KCNA5) mediates the ultra-rapid delayed rectifier current that controls atrial action potential duration. Given its atrial-specific expression and alterations in human atrial fibrillation, Kv1.5 has emerged as a promising target for the treatment of atrial fibrillation. A necessary step in the development of novel agents that selectively modulate trafficking pathways is the identification of the cellular machinery controlling Kv1.5 surface density, of which little is yet known. OBJECTIVE: To investigate the role of the unconventional myosin-V (MYO5A and MYO5B) motors in determining the cell surface density of Kv1.5. METHODS AND RESULTS: Western blot analysis showed MYO5A and MYO5B expression in the heart, whereas disruption of endogenous motors selectively reduced IKur current in adult rat cardiomyocytes. Dominant negative constructs and short hairpin RNA silencing demonstrated a role for MYO5A and MYO5B in the surface trafficking of Kv1.5 and connexin-43 but not potassium voltage-gated channel, subfamily H (eag-related), member 2 (KCNH2). Live-cell imaging of Kv1.5-GFP and retrospective labeling of phalloidin demonstrated motility of Kv1.5 vesicles on actin tracts. MYO5A participated in anterograde trafficking, whereas MYO5B regulated postendocytic recycling. Overexpression of mutant motors revealed a selective role for Rab11 in coupling MYO5B to Kv1.5 recycling. CONCLUSIONS: MYO5A and MYO5B control functionally distinct steps in the surface trafficking of Kv1.5. These isoform-specific trafficking pathways determine Kv1.5-encoded IKur in myocytes to regulate repolarizing current and, consequently, cardiac excitability. Therapeutic strategies that manipulate Kv1.5 selective trafficking pathways may prove useful in the treatment of arrhythmias.
Subject(s)
Cell Membrane/metabolism , Kv1.5 Potassium Channel/metabolism , Myocytes, Cardiac/metabolism , Myosin Heavy Chains/physiology , Myosin Type V/physiology , Myosins/physiology , Protein Transport/physiology , Actin Cytoskeleton/physiology , Animals , Arrhythmias, Cardiac/physiopathology , Cell Line , Connexin 43/analysis , ERG1 Potassium Channel , Endocytosis , Ether-A-Go-Go Potassium Channels/analysis , Gap Junctions , Genes, Reporter , Heart Conduction System/physiopathology , Ion Transport , Kv1.5 Potassium Channel/genetics , Male , Membrane Potentials/physiology , Mice , Mice, Inbred C57BL , Models, Cardiovascular , Myosin Heavy Chains/deficiency , Myosin Heavy Chains/genetics , Myosin Type V/deficiency , Myosin Type V/genetics , Myosins/deficiency , Myosins/genetics , Potassium/metabolism , Protein Isoforms/metabolism , RNA Interference , RNA, Small Interfering/pharmacology , Rats , Rats, Sprague-Dawley , Recombinant Fusion Proteins/metabolism , rab GTP-Binding Proteins/physiologyABSTRACT
An ever-increasing number of people world-wide are developing and suffering from heart failure, and existing therapies, although improved are not ideal. Therefore, innovative treatment strategies are urgently needed. As our understanding of the underlying dysfunction of the myocardium increases, so does our ability to target the mechanisms responsible for heart failure progression. In this review we discuss novel molecular therapies and approaches for the treatment of heart failure. We will focus on the G protein-coupled receptor kinase GRK2, an increasing target for heart failure therapy, based on its important role in disease progression and the therapeutic potential of GRK2 inhibitors.
