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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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2
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Garner AL. Contemporary Progress and Opportunities in RNA-Targeted Drug Discovery. ACS Med Chem Lett 2023; 14:251-259. [PMID: 36923915 PMCID: PMC10009794 DOI: 10.1021/acsmedchemlett.3c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The surprising discovery that RNAs are the predominant gene products to emerge from the human genome catalyzed a renaissance in RNA biology. It is now well-understood that RNAs act as more than just a messenger and comprise a large and diverse family of ribonucleic acids of differing sizes, structures, and functions. RNAs play expansive roles in the cell, contributing to the regulation and fine-tuning of nearly all aspects of gene expression and genome architecture. In line with the significance of these functions, we have witnessed an explosion in discoveries connecting RNAs with a variety of human diseases. Consequently, the targeting of RNAs, and more broadly RNA biology, has emerged as an untapped area of drug discovery, making the search for RNA-targeted therapeutics of great interest. In this Microperspective, I highlight contemporary learnings in the field and present my views on how to catapult us toward the systematic discovery of RNA-targeted medicines.
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Affiliation(s)
- Amanda L. Garner
- Department of Medicinal Chemistry,
College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, United States
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3
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Yang M, Carter S, Parmar S, Bume DD, Calabrese DR, Liang X, Yazdani K, Xu M, Liu Z, Thiele CJ, Schneekloth JS. Targeting a noncanonical, hairpin-containing G-quadruplex structure from the MYCN gene. Nucleic Acids Res 2021; 49:7856-7869. [PMID: 34289065 DOI: 10.1093/nar/gkab594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 11/12/2022] Open
Abstract
The MYCN gene encodes the transcription factor N-Myc, a driver of neuroblastoma (NB). Targeting G-quadruplexes (G4s) with small molecules is attractive strategy to control the expression of undruggable proteins such as N-Myc. However, selective binders to G4s are challenging to identify due to the structural similarity of many G4s. Here, we report the discovery of a small molecule ligand (4) that targets the noncanonical, hairpin containing G4 structure found in the MYCN gene using small molecule microarrays (SMMs). Unlike many G4 binders, the compound was found to bind to a pocket at the base of the hairpin region of the MYCN G4. This compound stabilizes the G4 and has affinity of 3.5 ± 1.6 μM. Moreover, an improved analog, MY-8, suppressed levels of both MYCN and MYCNOS (a lncRNA embedded within the MYCN gene) in NBEB neuroblastoma cells. This work indicates that the approach of targeting complex, hybrid G4 structures that exist throughout the human genome may be an applicable strategy to achieve selectivity for targeting disease-relevant genes including protein coding (MYCN) as well as non-coding (MYCNOS) gene products.
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Affiliation(s)
- Mo Yang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Sakereh Carter
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta D Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - David R Calabrese
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Xiao Liang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Kamyar Yazdani
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Man Xu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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4
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Hagler LD, Luu LM, Tonelli M, Lee J, Hayes SM, Bonson SE, Vergara JI, Butcher SE, Zimmerman SC. Expanded DNA and RNA Trinucleotide Repeats in Myotonic Dystrophy Type 1 Select Their Own Multitarget, Sequence-Selective Inhibitors. Biochemistry 2020; 59:3463-3472. [PMID: 32856901 DOI: 10.1021/acs.biochem.0c00472] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There are few methods available for the rapid discovery of multitarget drugs. Herein, we describe the template-assisted, target-guided discovery of small molecules that recognize d(CTG) in the expanded d(CTG·CAG) sequence and its r(CUG) transcript that cause myotonic dystrophy type 1. A positive cross-selection was performed using a small library of 30 monomeric alkyne- and azide-containing ligands capable of producing >5000 possible di- and trimeric click products. The monomers were incubated with d(CTG)16 or r(CUG)16 under physiological conditions, and both sequences showed selectivity in the proximity-accelerated azide-alkyne [3+2] cycloaddition click reaction. The limited number of click products formed in both selections and the even smaller number of common products suggests that this method is a useful tool for the discovery of single-target and multitarget lead therapeutic agents.
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Affiliation(s)
- Lauren D Hagler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Long M Luu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Marco Tonelli
- National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - JuYeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Samuel M Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sarah E Bonson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - J Ignacio Vergara
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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6
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Morgan BS, Sanaba BG, Donlic A, Karloff DB, Forte JE, Zhang Y, Hargrove AE. R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. ACS Chem Biol 2019; 14:2691-2700. [PMID: 31589399 DOI: 10.1021/acschembio.9b00631] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the opportunities available for targeting RNA with small molecules have been widely appreciated, the challenges associated with achieving specific RNA recognition in biological systems have hindered progress and prevented many researchers from entering the field. To facilitate the discovery of RNA-targeted chemical probes and their subsequent applications, we curated the RNA-targeted BIoactive ligaNd Database (R-BIND). This collection contains an array of information on reported chemical probes that target non-rRNA and have biological activity, and analysis has led to the discovery of RNA-privileged properties. Herein, we developed an online platform to make this information freely available to the community, offering search options, a suite of tools for probe development, and an updated R-BIND data set with detailed experimental information for each probe. We repeated the previous cheminformatics analysis on the updated R-BIND list and found that the distinguishing physicochemical, structural, and spatial properties remained unchanged, despite an almost 50% increase in the database size. Further, we developed several user-friendly tools, including queries based on cheminformatic parameters, experimental details, functional groups, and substructures. In addition, a nearest neighbor algorithm can assess the similarity of user-uploaded molecules to R-BIND ligands. These tools and resources can be used to design small molecule libraries, optimize lead ligands, or select targets, probes, assays, and control experiments. Chemical probes are critical to the study and discovery of novel functions for RNA, and we expect this resource to greatly assist researchers in exploring and developing successful RNA-targeted probes.
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Affiliation(s)
- Brittany S. Morgan
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Bilva G. Sanaba
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Anita Donlic
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Diane B. Karloff
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jordan E. Forte
- Wake Forest School of Medicine, 475 Vine Street, Winston Salem, North Carolina 27101, United States
| | - Yuqi Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
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7
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Calabrese DR, Zlotkowski K, Alden S, Hewitt WM, Connelly CM, Wilson RM, Gaikwad S, Chen L, Guha R, Thomas CJ, Mock BA, Schneekloth JS. Characterization of clinically used oral antiseptics as quadruplex-binding ligands. Nucleic Acids Res 2019; 46:2722-2732. [PMID: 29481610 PMCID: PMC5888870 DOI: 10.1093/nar/gky084] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/20/2018] [Indexed: 12/25/2022] Open
Abstract
Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a widely used oral antiseptic, and the G-quadruplex (G4) structure in the KRAS oncogene promoter. The interaction of chlorhexidine and related drugs to the KRAS G4 is evaluated using multiple biophysical methods, including thermal melt, fluorescence titration and surface plasmon resonance (SPR) assays. Chlorhexidine has a specific low micromolar binding interaction with the G4, while related drugs have weaker and/or less specific interactions. Through NMR experiments and docking studies, we propose a plausible binding mode driven by both aromatic stacking and groove binding interactions. Additionally, cancer cell lines harbouring oncogenic mutations in the KRAS gene exhibit increased sensitivity to chlorhexidine. Treatment of breast cancer cells with chlorhexidine decreases KRAS protein levels, while a KRAS gene transiently expressed by a promoter lacking a G4 is not affected. This work confirms that known ligands bind broadly to G4 structures, while other drugs and druglike compounds can have more selective interactions that may be biologically relevant.
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Katherine Zlotkowski
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Stephanie Alden
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Robert M Wilson
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Snehal Gaikwad
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892-4258, USA
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892-4258, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
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8
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Culf AS. Peptoids as tools and sensors. Biopolymers 2019; 110:e23285. [PMID: 31070792 DOI: 10.1002/bip.23285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 12/19/2022]
Abstract
A review of molecular tools and sensors assembled on N-substituted glycine, or α-peptoid, oligomers between 2013 and November 2018 with the following sections: (a) Peptoids as crystal growth modifiers, (b) Peptoids as catalysts, (c) Ion and molecule sequestration and transport, (d) Peptoid sensors, (e) Macromolecule recognition, (f) Cellular transporters, (g) Medical imaging, (h) Future direction and (i) Summary and outlook. Peptoids are a promising class of peptide mimic making them an excellent platform for functional molecule preparation. Attributes of peptoid oligomers include: (a) the ease of precise sequence definition and mono-dispersity; (b) access to a vast chemical space within simple and repeating chemical preparative steps and (c) thermal, chemical and biological stability all lending support for their application in a number of areas, with some that have been realised to date. The peptoid tool and sensor examples selected have realised practical utility. They serve to illustrate the rapidity of new insight that can generate in many disparate areas of science and technology, enabling the quick assembly of design criteria for efficient peptoid molecular tools and sensors.
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Affiliation(s)
- Adrian S Culf
- Sussex Research Laboratories, Inc., Ottawa, Ontario, Canada
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9
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Synthetic ligands for PreQ 1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure. Nat Commun 2019; 10:1501. [PMID: 30940810 PMCID: PMC6445138 DOI: 10.1038/s41467-019-09493-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Riboswitches are naturally occurring RNA aptamers that regulate gene expression by binding to specific small molecules. Riboswitches control the expression of essential bacterial genes and are important models for RNA-small molecule recognition. Here, we report the discovery of a class of synthetic small molecules that bind to PreQ1 riboswitch aptamers. These molecules bind specifically and reversibly to the aptamers with high affinity and induce a conformational change. Furthermore, the ligands modulate riboswitch activity through transcriptional termination despite no obvious chemical similarity to the cognate ligand. X-ray crystallographic studies reveal that the ligands share a binding site with the cognate ligand but make different contacts. Finally, alteration of the chemical structure of the ligand causes changes in the mode of RNA binding and affects regulatory function. Thus, target- and structure-based approaches can be used to identify and understand the mechanism of synthetic ligands that bind to and regulate complex, folded RNAs. RNA sensors—Riboswitches—respond to the binding of small molecules ligands through structure modification. Here the authors identify synthetic small molecules that bind and regulate the activity of PreQ1 Riboswitches despite having no obvious chemical similarity to the cognate ligand.
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10
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Huang Y, Huang Y, Zhang L, Chang A, Zhao P, Chai X, Wang J. Identification of crucial genes and prediction of small molecules for multidrug resistance of Hodgkin's lymphomas. Cancer Biomark 2019; 23:495-503. [PMID: 30347596 DOI: 10.3233/cbm-181496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Multidrug resistance of Hodgkin's lymphoma (HL) often results in recurrence. Thus, we aimed to explore the underlying molecular mechanisms of multidrug resistance using bioinformatics strategies. METHODS The gene expression profile was obtained from GEO database. Then, the differentially expressed genes were screened out, and their functional annotations were carried out. Then, gene-signal interaction network was constructed and Connectivity Map (CMAP) analysis was performed. RESULTS A total of 1425 dysregulated genes were screened out, which were mainly enriched in biological items, such as small molecule metabolic, signal transduction, and cell apoptosis. Some survival-related pathways, such as MAPK pathways, apoptosis, and P53 pathway, and several hub genes, such as PRKCA, ACTN1, PIP5K1B, PRKACB, and JAK2, might play key roles in the development of multidrug resistance. Interestingly, felodipine was predicted to be a potential agent overcoming the multidrug resistance. CONCLUSIONS The present study offered new insights into the molecular mechanisms of multidrug resistance and identified a series of important hub genes and small agents that might be critical for treatment of multidrug-resistant HL.
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Affiliation(s)
- Yi Huang
- Department of Internal Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China.,Department of Internal Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Yu Huang
- Department of Invasive Technology, Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou, China.,Department of Internal Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Liang Zhang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Aoshuang Chang
- School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Peng Zhao
- Department of Internal Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiao Chai
- Department of Internal Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Jishi Wang
- Department of Internal Medicine, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
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11
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A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context. Molecules 2019; 24:molecules24050946. [PMID: 30866557 PMCID: PMC6429135 DOI: 10.3390/molecules24050946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.
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12
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Li S, Li R, Ma Y, Zhang C, Huang T, Zhu S. Transcriptome analysis of differentially expressed genes and pathways associated with mitoxantrone treatment prostate cancer. J Cell Mol Med 2018; 23:1987-2000. [PMID: 30592148 PMCID: PMC6378179 DOI: 10.1111/jcmm.14100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022] Open
Abstract
The global physiological function of specifically expressed genes of mitoxantrone (MTX)‐resistant prostate cancer (PCa) is unclear. In this study, gene expression pattern from microarray data was investigated for identifying differentially expressed genes (DEGs) in MTX‐resistant PCa xenografts. Human PCa cell lines DU145 and PC3 were cultured in vitro and xenografted into severe combined immunodeficiency (SCID) mice, treated with MTX intragastrically, three times a week until all mice relapsed. Gene expression profiles of the xenografts from castrated mice were performed with Affymetrix human whole genomic oligonucleotide microarray. The Cytoscape software was used to investigate the relationship between proteins and the signalling transduction network. A total of 355 overlapping genes were differentially expressed in MTX‐resistant DU145R and PC3R xenografts. Of these, 16 genes were selected to be validated by quantitative real‐time PCR (qRT‐PCR) in these xenografts, and further tested in a set of formalin‐fixed, paraffin‐embedded and optimal cutting temperature (OCT) clinical tumour samples. Functional and pathway enrichment analyses revealed that these DEGs were closely related to cellular activity, androgen synthesis, DNA damage and repair, also involved in the ERK/MAPK, PI3K/serine‐threonine protein kinase, also known as protein kinase B, PKB (AKT) and apoptosis signalling pathways. This exploratory analysis provides information about potential candidate genes and may bring new insights into the molecular cascade involvement in MTX‐resistant PCa.
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Affiliation(s)
- Sanqiang Li
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Medical College, Henan University of Science and Technology, Luoyang, Henan, China
| | - Ruifang Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan, China
| | - Yu Ma
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Cong Zhang
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Tao Huang
- Cancer Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Sha Zhu
- Key laboratory of Infection and Immunization, Department of Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Collaborative Innovation Center of Cancer Chemoprevention, Zhengzhou, Henan, China
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13
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Yan S. Integrative analysis of promising molecular biomarkers and pathways for coronary artery disease using WGCNA and MetaDE methods. Mol Med Rep 2018; 18:2789-2797. [PMID: 30015926 PMCID: PMC6102698 DOI: 10.3892/mmr.2018.9277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/31/2018] [Indexed: 01/03/2023] Open
Abstract
The present study aimed to examine the molecular mechanisms of coronary artery disease (CAD). A total of four microarray datasets (training dataset no. GSE12288; validation dataset nos. GSE20680, GSE20681 and GSE42148) were downloaded from the Gene Expression Omnibus database, which included CAD and healthy samples. Weighted gene co-expression network analysis was applied to identify highly preserved modules across the four datasets. Differentially expressed genes (DEGs) with significant consistency in the four datasets were selected using the MetaDE method. The overlapping genes amongst the DEGs with significant consistency and in the preserved modules were used to construct a protein-protein interaction (PPI) network, followed by functional enrichment analysis. A total of 11 modules were established in the training dataset, and five of them were highly preserved across all four datasets, including 873 genes. There was a total of 836 DEGs with significant consistency in the four datasets. A total of 177 overlapping genes were selected, with which a PPI network was constructed. The top five genes of the PPI network were identified based on their degrees: LCK proto-oncogene, Src family tyrosine kinase (LCK), euchromatic histone lysine methyltransferase 2 (EHMT2), inosine monophosphate dehydrogenase 2 (IMPDH2), protein phosphatase 4 catalytic subunit (PPP4C) and ζ-chain of T-cell receptor associated protein kinase 70 (ZAP70). Genes in the PPI network were significantly involved in a number of Kyoto Encyclopedia Genes and Genomes pathways, including the ‘natural killer cell mediated cytotoxicity’, ‘primary immunodeficiency’ and ‘Fc gamma R-mediated phagocytosis’ pathways. LCK, EHMT2, IMPDH2, PPP4C and ZAP70 are suggested as promising molecular biomarkers for CAD. The ‘natural killer cell mediated cytotoxicity’, ‘primary immunodeficiency’ and ‘Fc gamma R-mediated phagocytosis’ pathways may serve important roles in CAD.
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Affiliation(s)
- Shilin Yan
- Department of Cardiology, Yangling Demonstration Zone Hospital, Xianyang, Shaanxi 712100, P.R. China
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14
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LeBlanc RM, Longhini AP, Tugarinov V, Dayie TK. NMR probing of invisible excited states using selectively labeled RNAs. JOURNAL OF BIOMOLECULAR NMR 2018; 71:165-172. [PMID: 29858959 DOI: 10.1007/s10858-018-0184-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments are invaluable for probing sparsely and transiently populated biomolecular states that cannot be directly detected by traditional NMR experiments and that are invisible by other biophysical approaches. A notable gap for RNA is the absence of CPMG experiments for measurement of methine base 1H and methylene C5' chemical shifts of ribose moieties in the excited state, partly because of complications from homonuclear 13C-13C scalar couplings. Here we present site-specific 13C labeling that makes possible the design of pulse sequences for recording accurate 1H-13C MQ and SQ CPMG experiments for ribose methine H1'-C1' and H2'-C2', base and ribose 1H CPMG, as well as a new 1H-13C TROSY-detected methylene (CH2) C5' CPMG relaxation pulse schemes. We demonstrate the utility of these experiments for two RNAs, the A-Site RNA known to undergo exchange and the IRE RNA suspected of undergoing exchange on microseconds to millisecond time-scale. We anticipate the new labeling approaches will facilitate obtaining structures of invisible states and provide insights into the relevance of such states for RNA-drug interactions.
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Affiliation(s)
- Regan M LeBlanc
- Department of Chemistry & Biochemistry, University of Maryland, College Park, 8314 Paint Branch Dr, College Park, MD, 20782, USA
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Andrew P Longhini
- Department of Chemistry & Biochemistry, University of Maryland, College Park, 8314 Paint Branch Dr, College Park, MD, 20782, USA
- University of California, Santa Barbara, CA, 93106, USA
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-052, USA
| | - T Kwaku Dayie
- Department of Chemistry & Biochemistry, University of Maryland, College Park, 8314 Paint Branch Dr, College Park, MD, 20782, USA.
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15
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Abstract
Click chemistry has emerged as a powerful tool in our arsenal for unlocking new biology. This includes its utility in both chemical biology and drug discovery. An emerging application of click chemistry is in the development of biochemical assays for high-throughput screening to identify new chemical probes and drug leads. This Feature Article will discuss the advancements in click chemistry that were necessary for the development of a new class of biochemical assay, catalytic enzyme-linked click chemistry assay or cat-ELCCA. Inspired by enzyme immunoassays, cat-ELCCA was designed as a click chemistry-based amplification assay where bioorthogonally-tagged analytes and enzymes are used in place of the enzyme-linked secondary antibodies used in immunoassays. The result is a robust assay format with demonstrated applicability in several important areas of biology and drug discovery, including post-translational modifications, pre-microRNA maturation, and protein-protein and RNA-protein interactions. Through the use of cat-ELCCA and other related click chemistry-based assays, new chemical probes for interrogating promising drug targets have been discovered. These examples will be discussed, in addition to a future outlook on the impact of this approach in probe and drug discovery.
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Affiliation(s)
- Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, USA.
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Affiliation(s)
- Bruce A Shapiro
- RNA Structure and Design Section, National Cancer Institute, Frederick, MD 21702, USA.
| | - Stuart F J Le Grice
- RT Biochemistry Section, National Cancer Institute, Frederick, MD 21702, USA.
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17
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Chen L, Sun F, Yang X, Jin Y, Shi M, Wang L, Shi Y, Zhan C, Wang Q. Correlation between RNA-Seq and microarrays results using TCGA data. Gene 2017; 628:200-204. [PMID: 28734892 DOI: 10.1016/j.gene.2017.07.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/20/2017] [Accepted: 07/19/2017] [Indexed: 02/05/2023]
Abstract
RNA sequencing (RNA-Seq) and microarray are two of the most commonly used high-throughput technologies for transcriptome profiling; however, they both have their own inherent strengths and limitations. This research aims to analyze the correlation between microarrays and RNA-Seq detection of transcripts in the same tissue sample to explore the reproducibility between the techniques. Using data of RNA-Seq v2 and three different microarrays provided by The Cancer Genome Atlas, 11,120 genes of 111 lung squamous cell carcinoma samples were simultaneously detected by the four methods. Then we analyzed the Pearson correlation between microarrays and RNA-Seq. Finally, in the six comparison results, 9984 (89.8%) genes, irrespective of which two methods were used, simultaneously showed the existence of correlation, whereas only 83 (0.1%) genes proved to have no significant correlation in either comparison. In addition, the comparisons between 3266 (29.3%) genes showed high correlation (R≥0.8) in all six comparisons, only for 1643 (14.8%) genes correlation were not as high in either comparison. Meanwhile, transcripts with extreme high or low expression levels were more highly discrepant across the methods. In conclusion, we found that, for most transcripts, the results obtained by RNA-Seq and microarrays were highly reproducible.
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Affiliation(s)
- Li Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China; Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Fenghao Sun
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Xiaodong Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Yulin Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Lin Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
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18
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Shortridge MD, Walker MJ, Pavelitz T, Chen Y, Yang W, Varani G. A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing. ACS Chem Biol 2017; 12:1611-1620. [PMID: 28437065 DOI: 10.1021/acschembio.7b00180] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) help orchestrate cellular growth and survival through post-transcriptional mechanisms. The dysregulation of miRNA biogenesis can lead to cellular growth defects and chemotherapeutic resistance and plays a direct role in the development of many chronic diseases. Among these RNAs, miR-21 is consistently overexpressed in most human cancers, leading to the down-regulation of key tumor-suppressing and pro-apoptotic factors, suggesting that inhibition of miR-21 biogenesis could reverse these negative effects. However, targeted inhibition of miR-21 using small molecules has had limited success. To overcome difficulties in targeting RNA secondary structure with small molecules, we developed a class of cyclic β-hairpin peptidomimetics which bind to RNA stem-loop structures, such as miRNA precursors, with potent affinity and specificity. We screened an existing cyclic peptide library and discovered a lead structure which binds to pre-miR21 with KD = 200 nM and prefers it over other pre-miRNAs. The NMR structure of the complex shows that the peptide recognizes the Dicer cleavage site and alters processing of the precursor to the mature miRNA in vitro and in cultured cells. The structure provides a rationale for the peptide binding activity and clear guidance for further improvements in affinity and targeting.
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Affiliation(s)
- Matthew D. Shortridge
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Matthew J. Walker
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Tom Pavelitz
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Yu Chen
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
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19
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Approaches for the Discovery of Small Molecule Ligands Targeting microRNAs. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA. J Med Chem 2016; 59:11148-11160. [PMID: 28002966 DOI: 10.1021/acs.jmedchem.6b01450] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Small molecules that bind to RNA potently and specifically are relatively rare. The study of molecules that bind to the HIV-1 transactivation response (TAR) hairpin, a cis-acting HIV genomic element, has long been an important model system for the chemistry of targeting RNA. Here we report the synthesis, biochemical, and structural evaluation of a series of molecules that bind to HIV-1 TAR RNA. A promising analogue, 15, retained the TAR binding affinity of the initial hit and displaced a Tat-derived peptide with an IC50 of 40 μM. NMR characterization of a soluble analogue, 2, revealed a noncanonical binding mode for this class of compounds. Finally, evaluation of 2 and 15 by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) indicates specificity in binding to TAR within the context of an in vitro-synthesized 365-nt HIV-1 5'-untranslated region (UTR). Thus, these compounds exhibit a novel and specific mode of interaction with TAR, providing important suggestions for RNA ligand design.
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