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      Sigma-1 Receptor (S1R) Interaction with Cholesterol: Mechanisms of S1R Activation and Its Role in Neurodegenerative Diseases

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          Abstract

          The sigma-1 receptor (S1R) is a 223 amino acid-long transmembrane endoplasmic reticulum (ER) protein. The S1R modulates the activity of multiple effector proteins, but its signaling functions are poorly understood. S1R is associated with cholesterol, and in our recent studies we demonstrated that S1R association with cholesterol induces the formation of S1R clusters. We propose that these S1R-cholesterol interactions enable the formation of cholesterol-enriched microdomains in the ER membrane. We hypothesize that a number of secreted and signaling proteins are recruited and retained in these microdomains. This hypothesis is consistent with the results of an unbiased screen for S1R-interacting partners, which we performed using the engineered ascorbate peroxidase 2 (APEX2) technology. We further propose that S1R agonists enable the disassembly of these cholesterol-enriched microdomains and the release of accumulated proteins such as ion channels, signaling receptors, and trophic factors from the ER. This hypothesis may explain the pleotropic signaling functions of the S1R, consistent with previously observed effects of S1R agonists in various experimental systems.

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          Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

          Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.
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            The mystery of membrane organization: composition, regulation and roles of lipid rafts

            Lipid rafts are relatively ordered membrane domains that are enriched in cholesterol and saturated lipids, and selectively recruit other lipids and proteins. They are dynamic and heterogeneous in composition and are thus challenging to visualize in vivo. New technologies are providing novel insights into the formation, organization and functions of these membrane domains.
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              DAVID-WS: a stateful web service to facilitate gene/protein list analysis

              Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions. Availability: The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html. Contact: xiaoli.jiao@nih.gov; rlempicki@nih.gov
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                15 April 2021
                April 2021
                : 22
                : 8
                : 4082
                Affiliations
                [1 ]Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Vladimir.Zhemkov@ 123456UTSouthwestern.edu
                [2 ]Prilenia Therapeutics Development LTD, Herzliya 4673304, Israel; Michal.Geva@ 123456prilenia.com (M.G.); Michael.Hayden@ 123456prilenia.com (M.R.H.)
                [3 ]Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, BC V6H 3V5, Canada
                [4 ]Laboratory of Molecular Neurodegeneration, Peter the Great St Petersburg State Polytechnic University, 195251 St. Petersburg, Russia
                Author notes
                Author information
                https://orcid.org/0000-0001-7006-6951
                Article
                ijms-22-04082
                10.3390/ijms22084082
                8071319
                33920913
                f7b5147e-b327-4f26-a2ba-1b97473f2c42
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

                History
                : 25 March 2021
                : 13 April 2021
                Categories
                Communication

                Molecular biology
                sigma-1 receptor,endoplasmic reticulum,mitochondria,contact sites,cholesterol,neurodegeneration,huntington’s disease,alzheimer’s disease,amyotrophic lateral sclerosis,drug target

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