1
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Xu X, Li Y, Han T, Zhao Y, Wang X, Fu X, Mao H. The hidden dangers of short-term glucocorticoid use in children: A genomic analysis. Int Immunopharmacol 2024; 135:112323. [PMID: 38788448 DOI: 10.1016/j.intimp.2024.112323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/11/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE Glucocorticoid (GC) administration has been associated with adverse drug reactions (ADRs) affecting multiple organ systems. While long-term use is widely recognized as a significant independent predictor of ADRs, it is important to note that even short-term use can lead to serious ADRs. The considerable inter-individual variability in ADRs occurrence may be influenced by genetic factors. This study, we present a case of a child who experienced significant weight gain and osteoporosis, following a brief administration of GC. METHODS To comprehensively investigate the underlying mechanisms, we conducted a genomic analysis utilizing the whole exome sequencing (WES) technique. This analysis encompassed the examination of phase I and phase II metabolism, influx transport, efflux transport, and drug targeting. Additionally, a comprehensive analysis was conducted on a cohort of 52,119 children to determine their ABCB1 rs1045642 genotype, and an additional 37,884 children were tested for their CYP3A5 rs776746 genotype. RESULTS The pharmacogenetic analysis unveiled the presence of a high-risk variant in ABCB1 rs1045642 and a slow metabolism variant in CYP3A5 rs776746, both of which have the potential to substantially contribute to ADRs. The findings of this study indicate that the prevalence of ABCB1 rs1045642 CT type among patients was 47.58%, with TT type accounting for 15.69 % and CC type accounting for 36.73 %. Furthermore, the distribution of CYP3A5 rs776746 CC genotype was observed in 50.54 % of individuals, while CT and TT genotypes were present in 41.15 % and 8.31 % of the population respectively. The distribution of ABCB1 and CYP3A5 genotypes among the pediatric population in China displays notable features. Specifically, for the ABCB1 rs1045642 genotype, less than 50 % of children exhibit intermediate metabotypes. Conversely, among children with the CYP3A5 rs776746 genotype, the predominant cause for enzyme activity is the slow metabolic type, accounting for up to 90 % of cases. CONCLUSIONS Consequently, it is imperative to thoroughly evaluate the impact of allele mutation on the effectiveness and safety of glucocorticoid drugs or other medications metabolized by the ABCB1 and CYP3A5, particularly in the context of Chinese pediatric patients.
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Affiliation(s)
- Xiaolin Xu
- Department of Immunity, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China; Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Yan Li
- Department of Immunity, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Tongxin Han
- Department of Immunity, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Yiming Zhao
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | - Xiaoling Wang
- Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China
| | | | - Huawei Mao
- Department of Immunity, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, China; Ministry of Education Key Laboratory of Major Diseases in Children, Beijing 100045, China.
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2
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Hu P, Liu Y, Zhu X, Kang H. ABCC Transporter Gene MoABC-R1 Is Associated with Pyraclostrobin Tolerance in Magnaporthe oryzae. J Fungi (Basel) 2023; 9:917. [PMID: 37755025 PMCID: PMC10532721 DOI: 10.3390/jof9090917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
Rice blast is a worldwide fungal disease that poses a threat to food security. Fungicide treatment is one of the most effective methods to control rice blast disease. However, the emergence of fungicide tolerance hampers the control efforts against rice blast. ATP-binding cassette (ABC) transporters have been found to be crucial in multidrug tolerance in various phytopathogenic fungi. This study investigated the association between polymorphisms in 50 ABC transporters and pyraclostrobin sensitivity in 90 strains of rice blast fungus. As a result, we identified MoABC-R1, a gene associated with fungicide tolerance. MoABC-R1 belongs to the ABCC-type transporter families. Deletion mutants of MoABC-R1, abc-r1, exhibited high sensitivity to pyraclostrobin at the concentration of 0.01 μg/mL. Furthermore, the pathogenicity of abc-r1 was significantly diminished. These findings indicate that MoABC-R1 not only plays a pivotal role in fungicide tolerance but also regulates the pathogenicity of rice blast. Interestingly, the combination of MoABC-R1 deletion with fungicide treatment resulted in a three-fold increase in control efficiency against rice blast. This discovery highlights MoABC-R1 as a potential target gene for the management of rice blast.
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Affiliation(s)
| | | | | | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (P.H.); (Y.L.); (X.Z.)
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3
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Lin K, Kong X, Tao X, Zhai X, Lv L, Dong D, Yang S, Zhu Y. Research Methods and New Advances in Drug-Drug Interactions Mediated by Renal Transporters. Molecules 2023; 28:5252. [PMID: 37446913 DOI: 10.3390/molecules28135252] [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: 05/31/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
The kidney is critical in the human body's excretion of drugs and their metabolites. Renal transporters participate in actively secreting substances from the proximal tubular cells and reabsorbing them in the distal renal tubules. They can affect the clearance rates (CLr) of drugs and their metabolites, eventually influence the clinical efficiency and side effects of drugs, and may produce drug-drug interactions (DDIs) of clinical significance. Renal transporters and renal transporter-mediated DDIs have also been studied by many researchers. In this article, the main types of in vitro research models used for the study of renal transporter-mediated DDIs are membrane-based assays, cell-based assays, and the renal slice uptake model. In vivo research models include animal experiments, gene knockout animal models, positron emission tomography (PET) technology, and studies on human beings. In addition, in vitro-in vivo extrapolation (IVIVE), ex vivo kidney perfusion (EVKP) models, and, more recently, biomarker methods and in silico models are included. This article reviews the traditional research methods of renal transporter-mediated DDIs, updates the recent progress in the development of the methods, and then classifies and summarizes the advantages and disadvantages of each method. Through the sorting work conducted in this paper, it will be convenient for researchers at different learning stages to choose the best method for their own research based on their own subject's situation when they are going to study DDIs mediated by renal transporters.
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Affiliation(s)
- Kexin Lin
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Xiaorui Kong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Xufeng Tao
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Xiaohan Zhai
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Linlin Lv
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Deshi Dong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Shilei Yang
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Yanna Zhu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
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4
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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5
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Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schäfer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA. The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells. SCIENCE ADVANCES 2022; 8:eabn6845. [PMID: 36223470 PMCID: PMC9555771 DOI: 10.1126/sciadv.abn6845] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/24/2022] [Indexed: 05/28/2023]
Abstract
Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.
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Affiliation(s)
- Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Dovile Januliene
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Kristian Parey
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Dario De Vecchis
- Center for Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Bianca Striednig
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Lars V. Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Arne Moeller
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Markus A. Seeger
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
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6
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Liu S, Storti M, Finazzi G, Bowler C, Dorrell RG. A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum. FRONTIERS IN PLANT SCIENCE 2022; 13:950467. [PMID: 36212359 PMCID: PMC9546453 DOI: 10.3389/fpls.2022.950467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.
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Affiliation(s)
- Shun Liu
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Mattia Storti
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Giovanni Finazzi
- Univ. Grenoble Alpes (UGA), Centre National Recherche Scientifique (CNRS), Commissariat Energie Atomique Energies Alternatives (CEA), Institut National Recherche Agriculture Alimentation Environnement (INRAE), Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National De La Recherche Scientifique (CNRS), Institut National De La Santé Et De La Recherche Médicale (INSERM), Université Paris Sciences et Lettres (PSL), Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, Paris, France
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7
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MsbA: an ABC transporter paradigm. Biochem Soc Trans 2021; 49:2917-2927. [PMID: 34821931 DOI: 10.1042/bst20211030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
ATP-binding cassette (ABC) transporters play an important role in various cellular processes. They display a similar architecture and share a mechanism which couples ATP hydrolysis to substrate transport. However, in the light of current data and recent experimental progress, this protein superfamily appears as multifaceted as their broad substrate range. Among the prokaryotic ABC transporters, MsbA can serve as a paradigm for research in this field. It is located in the inner membrane of Gram-negative bacteria and functions as a floppase for the lipopolysaccharide (LPS) precursor core-LPS, which is involved in the biogenesis of the bacterial outer membrane. While MsbA shows high similarity to eukaryotic ABC transporters, its expression in Gram-negative bacteria makes it conveniently accessible for many experimental approaches from spectroscopy to 3D structure determination. As an essential protein for bacterial membrane integrity, MsbA has also become an attractive target for the development of novel antibiotics. Furthermore, it serves as a model for multidrug efflux pumps. Here we provide an overview of recent findings and their relevance to the field, highlight the potential of methods such as solid-state NMR and EPR spectroscopy and provide a perspective for future work.
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8
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Thélot FA, Zhang W, Song K, Xu C, Huang J, Liao M. Distinct allosteric mechanisms of first-generation MsbA inhibitors. Science 2021; 374:580-585. [PMID: 34554829 DOI: 10.1126/science.abi9009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- François A Thélot
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
| | - Wenyi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, China.,Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - KangKang Song
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chen Xu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, China.,Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Maofu Liao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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9
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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10
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Identification of CTL Epitopes on Efflux Pumps of the ATP-Binding Cassette and the Major Facilitator Superfamily of Mycobacterium tuberculosis. J Immunol Res 2021; 2021:8899674. [PMID: 33490292 PMCID: PMC7803423 DOI: 10.1155/2021/8899674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/30/2020] [Accepted: 12/19/2020] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis is the world's most deadly infectious disease, with 10 million people falling ill and 1.5 million people dying from the disease every year. With the increasing number of drug-resistant Mycobacterium tuberculosis (MTB) strains and prevalence of coinfection of MTB with human immunodeficiency virus, many challenges remain in the prevention and treatment of tuberculosis. Therefore, the development of safe and effective tuberculosis vaccines is an urgent issue. In this study, we identified cytotoxic T lymphocyte epitopes on drug resistance-associated membrane protein efflux pumps of MTB, the ATP-binding cassette and the major facilitator superfamilies. First, three online software were used to predict HLA-A2-restricted epitopes. Then, the candidate epitopes were confirmed with the T2A2 cell binding affinity and peptide/MHC (pMHC) complex stability assays and in vitro immune activity experiments. Two drug-resistant T lymphocyte epitopes, designated Rv1218c-p24 and Rv2477c-p182, were selected, and their immunogenic activities studied in vivo in genetically engineered mice. The immune activities of these two epitopes were improved with the help of complete Freund's adjuvant (CFA). The epitopes identified here provide a foundation for the diagnosis and treatment of patients infected with drug resistant and the future development of a multiepitope vaccine.
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11
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Chen X, Wu H, Feng J, Li Y, Lv J, Shi W, Fan W, Xiao L, Sun D, Jiang M, Shi M. Transcriptome profiling unveils GAP43 regulates ABC transporters and EIF2 signaling in colorectal cancer cells. BMC Cancer 2021; 21:24. [PMID: 33402155 PMCID: PMC7786480 DOI: 10.1186/s12885-020-07728-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
Background The growth- and plasticity-associated protein-43 (GAP43) is biasedly expressed in indigestive system and nervous system. Recent study has shown that GAP43 is responsible for the development of neuronal growth and axonal regeneration in normal nervous tissue, while serves as a specific biomarker of relapsed or refractory neuroblastoma. However, its expression pattern and function in digestive system cancer remains to be clarified. Methods In this study, we examined the GAP43 status with qRT-PCR and bisulfite genomic sequencing in colorectal cancer (CRC). We investigated the effect of overexpressed GAP43 in CRC cells with RNA-seq. The RNA-seq data was analyzed with DAVID and IPA. Results GAP43 was downregulated in CRC compared to the adjacent tissues. DNA methylase inhibitor 5-Aza-CdR treatment could significantly induce GAP43, indicated that the silencing of GAP43 gene in CRC is closely related to DNA methylation. Bisulfite genomic sequencing confirmed the promoter methylation of GAP43 in CRC. To explore the transcriptional alterations by overexpressed GAP43 in CRC, we performed RNA-seq and found that upregulated genes were significantly enriched in the signaling pathways of ABC transporters and ECM-receptor interaction, while downregulated genes were significantly enriched in Ribosome signaling pathway. Further Ingenuity Pathway Analysis (IPA) showed that EIF2 signaling pathway was significantly repressed by overexpression of GAP43. Conclusion Our findings provide a novel mechanistic insight of GAP43 in CRC. Transcriptome profiling of overexpressed GAP43 in CRC uncovered the functional roles of GAP43 in the development of human CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07728-x.
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Affiliation(s)
- Xi Chen
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Hongjin Wu
- Department of Clinical Laboratory, Hangzhou Cancer Hospital, Hangzhou,, 320000, Zhejiang, China.,The NHC Key Laboratory of Drug Addition Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China
| | - Jia Feng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Ying Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Jiao Lv
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Weikai Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Weiwei Fan
- Department of Infectious and Medicine, Heilongjiang Provincial Hospital, Harbin, 150036, China
| | - Li Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Danmeng Sun
- Department of Pediatrics, Data People's hospital, Shenmu, 719301, China
| | - Mingfeng Jiang
- Department of Clinical Laboratory, Hangzhou Cancer Hospital, Hangzhou,, 320000, Zhejiang, China.
| | - Ming Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
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12
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Jones PM, George AM. Is the emperor wearing shorts? The published structures of ABC transporters. FEBS Lett 2020; 594:3790-3798. [PMID: 32981041 DOI: 10.1002/1873-3468.13941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/24/2020] [Accepted: 09/13/2020] [Indexed: 12/20/2022]
Abstract
ABC transporters use the energy of ATP binding and hydrolysis to transport substrates across cellular membranes. They comprise two highly conserved nucleotide binding domains and two transmembrane domains that form the transmembrane channel and contain the substrate binding sites. Structural analyses have found a variety of seemingly unrelated folds for the ABC transporter transmembrane domains, and from these, a set of diverse mechanistic models has been inferred. Nevertheless, in spite of the explosion in structure determination of ABC transporters in the last decade, advancement in certainty and clarity as to fundamental aspects of their molecular mechanisms remains elusive. With this in mind, here we put and examine the question: Could current ABC structures differ from the physiologic membrane-embedded forms?
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
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13
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ATP-dependent thermostabilization of human P-glycoprotein (ABCB1) is blocked by modulators. Biochem J 2020; 476:3737-3750. [PMID: 31774117 DOI: 10.1042/bcj20190736] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/13/2019] [Accepted: 11/27/2019] [Indexed: 11/17/2022]
Abstract
P-glycoprotein (P-gp), an ATP-binding cassette transporter associated with multidrug resistance in cancer cells, is capable of effluxing a number of xenobiotics as well as anticancer drugs. The transport of molecules through the transmembrane (TM) region of P-gp involves orchestrated conformational changes between inward-open and inward-closed forms, the details of which are still being worked out. Here, we assessed how the binding of transport substrates or modulators in the TM region and the binding of ATP to the nucleotide-binding domains (NBDs) affect the thermostability of P-gp in a membrane environment. P-gp stability after exposure at high temperatures (37-80°C) was assessed by measuring ATPase activity and loss of monomeric P-gp. Our results show that P-gp is significantly thermostabilized (>22°C higher IT50) by the binding of ATP under non-hydrolyzing conditions (in the absence of Mg2+). By using an ATP-binding-deficient mutant (Y401A) and a hydrolysis-deficient mutant (E556Q/E1201Q), we show that thermostabilization of P-gp requires binding of ATP to both NBDs and their dimerization. Additionally, we found that transport substrates do not affect the thermal stability of P-gp either in the absence or presence of ATP; in contrast, inhibitors of P-gp including tariquidar and zosuquidar prevent ATP-dependent thermostabilization in a concentration-dependent manner, by stabilizing the inward-open conformation. Altogether, our data suggest that modulators, which bind in the TM regions, inhibit ATP hydrolysis and drug transport by preventing the ATP-dependent dimerization of the NBDs of P-gp.
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14
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Rozo AJ, Cox MH, Devitt A, Rothnie AJ, Goddard AD. Biophysical analysis of lipidic nanoparticles. Methods 2020; 180:45-55. [PMID: 32387313 DOI: 10.1016/j.ymeth.2020.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 12/18/2022] Open
Abstract
Biological nanoparticles include liposomes, extracellular vesicle and lipid-based discoidal systems. When studying such particles, there are several key parameters of interest, including particle size and concentration. Measuring these characteristics can be of particular importance in the research laboratory or when producing such particles as biotherapeutics. This article briefly describes the major types of lipid-containing nanoparticles and the techniques that can be used to study them. Such methodologies include electron microscopy, atomic force microscopy, dynamic light scattering, nanoparticle tracking analysis, flow cytometry, tunable resistive pulse sensing and microfluidic resistive pulse sensing. Whilst no technique is perfect for the analysis of all nanoparticles, this article provides advantages and disadvantages of each, highlighting the latest developments in the field. Finally, we demonstrate the use of microfluidic resistive pulse sensing for the analysis of biological nanoparticles.
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Affiliation(s)
- Annaïg J Rozo
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Megan H Cox
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK; Meritics Ltd, Unit 3, Clipstone Brook Industrial Estate, Cherrycourt Way, Leighton Buzzard LU7 4GP, UK
| | - Andrew Devitt
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Alan D Goddard
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
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15
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Eckenstaler R, Benndorf RA. 3D structure of the transporter ABCG2-What's new? Br J Pharmacol 2020; 177:1485-1496. [PMID: 31985041 PMCID: PMC7060357 DOI: 10.1111/bph.14991] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/20/2019] [Accepted: 01/07/2020] [Indexed: 12/13/2022] Open
Abstract
ABCG2 belongs to the ABC transporter superfamily and functions as a poly-specific efflux pump. As it can transport a broad spectrum of substrates out of cells, ABCG2 is thought to alter the pharmacokinetics of drugs applied to treat certain diseases. Especially, its potential to induce resistance to chemotherapy is currently the object of intense research. To foster understanding of mechanisms relevant for substrate recognition and selection of ABCG2 substrates and to finally develop selective therapeutic modulators (e.g. inhibitors) of ABCG2 transport activity, it is important to further explore the precise 3D structure of the transporter. While efforts to elucidate the three-dimensional structure of ABCG2 using X-ray crystal structure analysis have not been successful so far, high-resolution cryo-electron microscopy-based investigations have revealed exciting new insights into the structure and function of the transporter. In this review, we will focus on these seminal publications to summarize the current understanding of tertiary and quaternary structure, homodimerization or oligomerization, and functions of the ABCG2 transporter protein.
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Affiliation(s)
| | - Ralf A Benndorf
- Institute of Pharmacy, Martin-Luther-University, Halle, Germany
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16
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Beis K, Rebuffat S. Multifaceted ABC transporters associated to microcin and bacteriocin export. Res Microbiol 2019; 170:399-406. [DOI: 10.1016/j.resmic.2019.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 12/30/2022]
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