Chemogenomic profiling is a powerful and unbiased approach to elucidate pharmacological targets and the mechanism of bioactive compounds. It is based on identifying cellular hypersensitivity and resistance caused by individual gene modulations with genome-wide coverage. Due to the requirement of bar-coded, genome-wide deletion collections, high-resolution experiments of this nature have historically been limited to fungal systems. Pooled RNAi reagents have enabled similar attempts in mammalian cells but efforts have been hampered by significant off-target effects and experimental noise. The CRISPR/Cas9 system for the first time enables precise DNA editing at defined loci in a genome-wide fashion. Here we present the detailed protocol that leverages the CRISPR/Cas9 system for chemogenomic profiling and target identification of diverse chemical probes.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-4939-8891-4_9 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Exploring the Antimycobacterial Potential of Podocarpusflavone A from : In Vitro and In Vivo Insights.
Pharmaceuticals (Basel)
November 2024
Laboratório de Produtos Bioativos (LPBio), Instituto de Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé 27930-560, RJ, Brazil.
: Tuberculosis (TB) is one of the leading infectious causes of death worldwide, highlighting the importance of identifying new anti-TB agents. In previous research, our team identified antimycobacterial activity in leaf extract; therefore, this study aims to conduct further exploration of its potential. : Classical chromatography was applied for fractionation and spectrometric techniques were utilized for chemical characterization.
View Article and Find Full Text PDFScreening of a kinase inhibitor library identified novel targetable kinase pathways in triple-negative breast cancer.
Anticancer Drugs
January 2025
Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX.
Triple-negative breast cancer (TNBC) is a highly invasive breast cancer subtype that is challenging to treat due to inherent heterogeneity and absence of estrogen, progesterone, and human epidermal growth factor 2 receptors. Kinase signaling networks drive cancer growth and development, and kinase inhibitors are promising anti-cancer strategies in diverse cancer subtypes. Kinase inhibitor screens are an efficient, valuable means of identifying compounds that suppress cancer cell growth in vitro , facilitating the identification of kinase vulnerabilities to target therapeutically.
View Article and Find Full Text PDFToward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open.
RSC Med Chem
November 2024
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt Frankfurt 60438 Germany
Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public-private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents.
View Article and Find Full Text PDFIdentification of small molecule agonists of fetal hemoglobin expression for the treatment of sickle cell disease.
PLoS One
November 2024
Takeda Development Center Americas, Inc., San Diego, California, United States of America.
Induction of fetal hemoglobin (HbF) has been shown to be a viable therapeutic approach to treating sickle cell disease and potentially other β-hemoglobinopathies. To identify targets and target-modulating small molecules that enhance HbF expression, we engineered a human umbilical-derived erythroid progenitor reporter cell line (HUDEP2_HBG1_HiBiT) by genetically tagging a HiBiT peptide to the carboxyl (C)-terminus of the endogenous HBG1 gene locus, which codes for γ-globin protein, a component of HbF. Employing this reporter cell line, we performed a chemogenomic screen of approximately 5000 compounds annotated with known targets or mechanisms that have achieved clinical stage or approval by the US Food and Drug Administration (FDA).
View Article and Find Full Text PDFAnalysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology.
Nat Genet
September 2024
Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
Tumor genomic profiling is increasingly seen as a prerequisite to guide the treatment of patients with cancer. To explore the value of whole-genome sequencing (WGS) in broadening the scope of cancers potentially amenable to a precision therapy, we analysed whole-genome sequencing data on 10,478 patients spanning 35 cancer types recruited to the UK 100,000 Genomes Project. We identified 330 candidate driver genes, including 74 that are new to any cancer.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!