1
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Sakellakis M. Orphan receptors in prostate cancer. Prostate 2022; 82:1016-1024. [PMID: 35538397 DOI: 10.1002/pros.24370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND The identification of new cellular receptors has been increasing rapidly. A receptor is called "orphan" if an endogenous ligand has not been identified yet. METHODS Here we review receptors that contribute to prostate cancer and are considered orphan or partially orphan. This means that the full spectrum of their endogenous ligands remains unknown. RESULTS The orphan receptors are divided into two major families. The first group includes G protein-coupled receptors. Most are orphan olfactory receptors. OR51E1 inhibits cell proliferation and induces senescence in prostate cancer. OR51E2 inhibits prostate cancer growth, but promotes invasiveness and metastasis. GPR158, GPR110, and GPCR-X play significant roles in prostate cancer development and progression. However, GPR160 induces cell cycle arrest and apoptosis. The other major subset of orphan receptors are nuclear receptors. Receptor-related orphan receptor α (RORα) inhibits tumor growth, but RORγ stimulates androgen receptor signaling. PXR contributes to metabolic deactivation of androgens and inhibits cell proliferation. TLX has protumorigenic effects in prostate cancer, while its knockdown triggers cellular senescence and growth arrest. Estrogen-related receptor ERRγ can inhibit tumor growth but ERRα is protumorigenic. Dax1 and short heterodimeric partner are also inhibitory in prostate cancer. CONCLUSION There is a "zoo" of relatively underappreciated orphan receptors that play key roles in prostate cancer.
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Affiliation(s)
- Minas Sakellakis
- Fourth Oncology Department and Comprehensive Clinical Trials Center, Metropolitan Hospital, Athens, Greece
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2
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Kalra R, Tiwari D, Dkhar HK, Bhagyaraj E, Kumar R, Bhardwaj A, Gupta P. Host factors subverted by Mycobacterium tuberculosis: Potential targets for host directed therapy. Int Rev Immunol 2021; 42:43-70. [PMID: 34678117 DOI: 10.1080/08830185.2021.1990277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Despite new approaches in the diagnosis and treatment of tuberculosis (TB), it continues to be a major health burden. Several immunotherapies that potentiate the immune response have come up as adjuncts to drug therapies against drug resistant TB strains; however, there needs to be an urgent appraisal of host specific drug targets for improving their clinical management and to curtail disease progression. Presently, various host directed therapies (HDTs) exist (repurposed drugs, nutraceuticals, monoclonal antibodies and immunomodulatory agents), but these mostly address molecules that combat disease progression. AREAS COVERED The current review discusses major Mycobacterium tuberculosis (M. tuberculosis) survival paradigms inside the host and presents a plethora of host targets subverted by M. tuberculosis which can be further explored for future HDTs. The host factors unique to M. tuberculosis infection (in humans) have also been identified through an in-silico interaction mapping. EXPERT OPINION HDTs could become the next-generation adjunct therapies in order to counter antimicrobial resistance and virulence, as well as to reduce the duration of existing TB treatments. However, current scientific efforts are largely directed toward combatants rather than host molecules co-opted by M. tuberculosis for its survival. This might drive the immune system to a hyper-inflammatory condition; therefore, we emphasize that host factors subverted by M. tuberculosis, and their subsequent neutralization, must be considered for development of better HDTs.
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Affiliation(s)
- Rashi Kalra
- Department of Molecular Biology, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Drishti Tiwari
- Department of Molecular Biology, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Hedwin Kitdorlang Dkhar
- Department of Molecular Biology, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Ella Bhagyaraj
- Department of Molecular Biology, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Rakesh Kumar
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Anshu Bhardwaj
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Pawan Gupta
- Department of Molecular Biology, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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3
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Behl T, Kaur I, Sehgal A, Singh S, Bhatia S, Al-Harrasi A, Zengin G, Babes EE, Brisc C, Stoicescu M, Toma MM, Sava C, Bungau SG. Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. Int J Mol Sci 2021; 22:6184. [PMID: 34201152 PMCID: PMC8227524 DOI: 10.3390/ijms22126184] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 02/01/2023] Open
Abstract
With advanced technology and its development, bioinformatics is one of the avant-garde fields that has managed to make amazing progress in the pharmaceutical-medical field by modeling the infrastructural dimensions of healthcare and integrating computing tools in drug innovation, facilitating prevention, detection/more accurate diagnosis, and treatment of disorders, while saving time and money. By association, bioinformatics and pharmacovigilance promoted both sample analyzes and interpretation of drug side effects, also focusing on drug discovery and development (DDD), in which systems biology, a personalized approach, and drug repositioning were considered together with translational medicine. The role of bioinformatics has been highlighted in DDD, proteomics, genetics, modeling, miRNA discovery and assessment, and clinical genome sequencing. The authors have collated significant data from the most known online databases and publishers, also narrowing the diversified applications, in order to target four major areas (tetrad): DDD, anti-microbial research, genomic sequencing, and miRNA research and its significance in the management of current pandemic context. Our analysis aims to provide optimal data in the field by stratification of the information related to the published data in key sectors and to capture the attention of researchers interested in bioinformatics, a field that has succeeded in advancing the healthcare paradigm by introducing developing techniques and multiple database platforms, addressed in the manuscript.
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Affiliation(s)
- Tapan Behl
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Ishnoor Kaur
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Aayush Sehgal
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Sukhbir Singh
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India; (I.K.); (A.S.); (S.S.)
| | - Saurabh Bhatia
- Amity Institute of Pharmacy, Amity University, Gurugram 122413, India;
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 616, Oman;
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Centre, University of Nizwa, Birkat Al Mauz, Nizwa 616, Oman;
| | - Gokhan Zengin
- Department of Biology, Faculty of Science, Selcuk University Campus, 42130 Konya, Turkey;
| | - Elena Emilia Babes
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Ciprian Brisc
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Manuela Stoicescu
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Mirela Marioara Toma
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
| | - Cristian Sava
- Department of Medical Disciplines, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania; (E.E.B.); (C.B.); (M.S.); (C.S.)
| | - Simona Gabriela Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
- Doctoral School of Biomedical Sciences, University of Oradea, 410087 Oradea, Romania
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4
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Tiwari D, Gupta P. Nuclear Receptors in Asthma: Empowering Classical Molecules Against a Contemporary Ailment. Front Immunol 2021; 11:594433. [PMID: 33574813 PMCID: PMC7870687 DOI: 10.3389/fimmu.2020.594433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
The escalation in living standards and adoption of 'Western lifestyle' has an allied effect on the increased allergy and asthma burden in both developed and developing countries. Current scientific reports bespeak an association between allergic diseases and metabolic dysfunction; hinting toward the critical requirement of organized lifestyle and dietary habits. The ubiquitous nuclear receptors (NRs) translate metabolic stimuli into gene regulatory signals, integrating diet inflences to overall developmental and physiological processes. As a consequence of such promising attributes, nuclear receptors have historically been at the cutting edge of pharmacy world. This review discusses the recent findings that feature the cardinal importance of nuclear receptors and how they can be instrumental in modulating current asthma pharmacology. Further, it highlights a possible future employment of therapy involving dietary supplements and synthetic ligands that would engage NRs and aid in eliminating both asthma and linked comorbidities. Therefore, uncovering new and evolving roles through analysis of genomic changes would represent a feasible approach in both prevention and alleviation of asthma.
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Affiliation(s)
| | - Pawan Gupta
- Department of Molecular Biology, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
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5
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Pham B, Arons AB, Vincent JG, Fernandez EJ, Shen T. Regulatory Mechanics of Constitutive Androstane Receptors: Basal and Ligand-Directed Actions. J Chem Inf Model 2019; 59:5174-5182. [PMID: 31714771 DOI: 10.1021/acs.jcim.9b00695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Constitutive androstane receptor (CAR) is a nuclear hormone receptor that primarily functions in sensing and metabolizing xenobiotics. The basal activity of this receptor is relatively high, and CAR is deemed active in the absence of ligand. The (over)activation can promote drug toxicity and tumor growth. Thus, therapeutic treatments seek inverse agonists to inhibit or modulate CAR activities. To advance our understanding of the regulatory mechanisms of CAR, we used computational and experimental approaches to elucidate three aspects of CAR activation and inactivation: (1) ligand-dependent actions, (2) ligand-orthologue specificity, and (3) constitutive activity. For ligand-dependent actions, we examined the ligand-bound simulations and identified two sets of ligand-induced contacts promoting CAR activation via coactivator binding (H11-H12 contact) or inactivation via corepressor binding (H4-H11 contact). For orthologue specificity, we addressed a puzzling fact that murine CAR (mCAR) and human CAR (hCAR) respond differently to the same ligand (CITCO), despite their high sequence homology. We found that the helix H7 of hCAR is responsible for a stronger binding of the ligand CITCO compared to mCAR, hence a stronger CITCO-induced activation. For basal activity, we reported computer-generated unliganded CAR structures and critical mutagenesis (mCAR's V209A and N333D) results of a cell-based transcription assay. Our results reveal that the basal conformation of CAR shares prominent features with the agonist-bound form, and helix HX has an important contribution to the constitutive activity. These findings altogether can be useful for the understanding of constitutively active receptors and the design of drug molecules targeting them.
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Affiliation(s)
- Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Avery Bancroft Arons
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Jeremy G Vincent
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Elias J Fernandez
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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6
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Nanduri R, Kalra R, Bhagyaraj E, Chacko AP, Ahuja N, Tiwari D, Kumar S, Jain M, Parkesh R, Gupta P. AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy. Autophagy 2019; 15:1280-1295. [PMID: 30669929 DOI: 10.1080/15548627.2019.1571717] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Macroautophagy/autophagy is a complex self-degradative mechanism responsible for clearance of non functional organelles and proteins. A range of factors influences the autophagic process, and disruptions in autophagy-related mechanisms lead to disease states, and further exacerbation of disease. Despite in-depth research into autophagy and its role in pathophysiological processes, the resources available to use it for therapeutic purposes are currently lacking. Herein we report the Autophagy Small Molecule Database (AutophagySMDB; http://www.autophagysmdb.org/ ) of small molecules and their cognate protein targets that modulate autophagy. Presently, AutophagySMDB enlists ~10,000 small molecules which regulate 71 target proteins. All entries are comprised of information such as EC50 (half maximal effective concentration), IC50 (half maximal inhibitory concentration), Kd (dissociation constant) and Ki (inhibition constant), IUPAC name, canonical SMILE, structure, molecular weight, QSAR (quantitative structure activity relationship) properties such as hydrogen donor and acceptor count, aromatic rings and XlogP. AutophagySMDB is an exhaustive, cross-platform, manually curated database, where either the cognate targets for small molecule or small molecules for a target can be searched. This database is provided with different search options including text search, advanced search and structure search. Various computational tools such as tree tool, cataloging tools, and clustering tools have also been implemented for advanced analysis. Data and the tools provided in this database helps to identify common or unique scaffolds for designing novel drugs or to improve the existing ones for autophagy small molecule therapeutics. The approach to multitarget drug discovery by identifying common scaffolds has been illustrated with experimental validation. Abbreviations: AMPK: AMP-activated protein kinase; ATG: autophagy related; AutophagySMDB: autophagy small molecule database; BCL2: BCL2, apoptosis regulator; BECN1: beclin 1; CAPN: calpain; MTOR: mechanistic target of rapamycin kinase; PPARG: peroxisome proliferator activated receptor gamma; SMILES: simplified molecular input line entry system; SQSTM1: sequestosome 1; STAT3: signal transducer and activator of transcription.
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Affiliation(s)
- Ravikanth Nanduri
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Rashi Kalra
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Ella Bhagyaraj
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Anuja P Chacko
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Nancy Ahuja
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Drishti Tiwari
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Sumit Kumar
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Monika Jain
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Raman Parkesh
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
| | - Pawan Gupta
- a Department of Molecular Biology , CSIR-Institute of Microbial Technology , Chandigarh , India
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7
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Réau M, Lagarde N, Zagury JF, Montes M. Nuclear Receptors Database Including Negative Data (NR-DBIND): A Database Dedicated to Nuclear Receptors Binding Data Including Negative Data and Pharmacological Profile. J Med Chem 2018; 62:2894-2904. [PMID: 30354114 DOI: 10.1021/acs.jmedchem.8b01105] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nuclear receptors (NRs) are transcription factors that regulate gene expression in various physiological processes through their interactions with small hydrophobic molecules. They constitute an important class of targets for drugs and endocrine disruptors and are widely studied for both health and environment concerns. Since the integration of negative data can be critical for accurate modeling of ligand activity profiles, we manually collected and annotated NRs interaction data (positive and negative) through a sharp review of the corresponding literature. 15 116 positive and negative interactions data are provided for 28 NRs together with 593 PDB structures in the freely available Nuclear Receptors Database Including Negative Data ( http://nr-dbind.drugdesign.fr ). The NR-DBIND contains the most extensive information about interaction data on NRs, which should bring valuable information to chemists, biologists, pharmacologists and toxicologists.
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Affiliation(s)
- Manon Réau
- Laboratoire GBA, EA4627 , Conservatoire National des Arts et Métiers , 2 Rue Conté , 75003 Paris , France
| | - Nathalie Lagarde
- Laboratoire GBA, EA4627 , Conservatoire National des Arts et Métiers , 2 Rue Conté , 75003 Paris , France.,Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques in Silico, INSERM UMR-S 973, 75205 Paris , France
| | - Jean-François Zagury
- Laboratoire GBA, EA4627 , Conservatoire National des Arts et Métiers , 2 Rue Conté , 75003 Paris , France
| | - Matthieu Montes
- Laboratoire GBA, EA4627 , Conservatoire National des Arts et Métiers , 2 Rue Conté , 75003 Paris , France
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8
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Mazaira GI, Zgajnar NR, Lotufo CM, Daneri-Becerra C, Sivils JC, Soto OB, Cox MB, Galigniana MD. The Nuclear Receptor Field: A Historical Overview and Future Challenges. NUCLEAR RECEPTOR RESEARCH 2018; 5:101320. [PMID: 30148160 PMCID: PMC6108593 DOI: 10.11131/2018/101320] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In this article we summarize the birth of the field of nuclear receptors, the discovery of untransformed and transformed isoforms of ligand-binding macromolecules, the discovery of the three-domain structure of the receptors, and the properties of the Hsp90-based heterocomplex responsible for the overall structure of the oligomeric receptor and many aspects of the biological effects. The discovery and properties of the subfamily of receptors called orphan receptors is also outlined. Novel molecular aspects of the mechanism of action of nuclear receptors and challenges to resolve in the near future are discussed.
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Affiliation(s)
- Gisela I. Mazaira
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (1428), Argentina
| | - Nadia R. Zgajnar
- Instituto de Biología y Medicina Experimental- CONICET. Buenos Aires (1428), Argentina
| | - Cecilia M. Lotufo
- Instituto de Biología y Medicina Experimental- CONICET. Buenos Aires (1428), Argentina
| | | | - Jeffrey C. Sivils
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Olga B. Soto
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Marc B. Cox
- Department of Biological Sciences and Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Mario D. Galigniana
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (1428), Argentina
- Instituto de Biología y Medicina Experimental- CONICET. Buenos Aires (1428), Argentina
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9
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Qiu T, Wu D, Qiu J, Cao Z. Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on proteochemometric modelling. J Cheminform 2018; 10:21. [PMID: 29651663 PMCID: PMC5897275 DOI: 10.1186/s13321-018-0275-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 04/02/2018] [Indexed: 02/10/2023] Open
Abstract
Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specific genes and associated with various diseases, which make it essential drug targets. Approaches which can predict the inhibition ability of compounds for different NR target should be particularly helpful for drug development. In this study, proteochemometric modelling was introduced to analysis the bioactivity between chemical compounds and NR targets. Results illustrated the ability of our PCM model for high-throughput NR-inhibitor screening after evaluated on both internal (AUC > 0.870) and external (AUC > 0.746) validation set. Moreover, in-silico predicted bioactive compounds were clustered according to structure similarity and a series of representative molecular scaffolds can be derived for five major NR targets. Through scaffolds analysis, those essential bioactive scaffolds of different NR target can be detected and compared. Generally, the methods and molecular scaffolds proposed in this article can not only help the screening of potential therapeutic NR-inhibitors but also able to guide the future NR-related drug discovery.
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Affiliation(s)
- Tianyi Qiu
- School of Life Sciences and Technology, Shanghai 10th People's Hospital, Tongji University, No. 1239 SiPing Road, Shanghai, China.,The Institute of Biomedical Sciences, Fudan University, No. 138 Medical College Road, Shanghai, China
| | - Dingfeng Wu
- School of Life Sciences and Technology, Shanghai 10th People's Hospital, Tongji University, No. 1239 SiPing Road, Shanghai, China
| | - Jingxuan Qiu
- School of Life Sciences and Technology, Shanghai 10th People's Hospital, Tongji University, No. 1239 SiPing Road, Shanghai, China.,School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, No. 516 JunGong Road, Shanghai, China
| | - Zhiwei Cao
- School of Life Sciences and Technology, Shanghai 10th People's Hospital, Tongji University, No. 1239 SiPing Road, Shanghai, China.
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10
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Saini A, Mahajan S, Ahuja N, Bhagyaraj E, Kalra R, Janmeja AK, Gupta P. An Accord of Nuclear Receptor Expression in M. tuberculosis Infected Macrophages and Dendritic Cells. Sci Rep 2018; 8:2296. [PMID: 29396519 PMCID: PMC5797181 DOI: 10.1038/s41598-018-20769-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/23/2018] [Indexed: 12/28/2022] Open
Abstract
Mycobacterium tuberculosis instigates interactions with host factors to promote its survival within the host inimical conditions. Among such factors, nuclear receptors (NRs) seem to be promising candidates owing to their role in bacterial pathogenesis. However, only few members of NR superfamily have been implicated in M. tuberculosis infection and there is a dearth of comprehensive knowledge about expression or function of the entire superfamily. In this study, we performed detailed expression analysis and identified key NRs getting differentially regulated in murine macrophages and dendritic cells (DC) upon infection with H37Rv. The murine macrophages and DCs infected with H37Rv entailed overlapping changes in the expression of certain NRs which reflect upon the possibility that both cells might utilize similar transcriptional programs upon M. tuberculosis infection. We identified Nr4a3 and Rora, which have not been implicated in M. tuberculosis pathogenesis, undergo similar changes in expression in macrophages and DCs upon H37Rv infection. Interestingly, a similar pattern in their expression was also observed in infected human monocyte derived macrophages and the findings corroborated well with PBMCs obtained from TB patients. This all-inclusive analysis provides the basis for a precise approach in identifying NRs that can be targeted therapeutically in intracellular bacterial infections.
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Affiliation(s)
- Ankita Saini
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sahil Mahajan
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India.,Department of Orthopedics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nancy Ahuja
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India
| | - Ella Bhagyaraj
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India
| | - Rashi Kalra
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India
| | | | - Pawan Gupta
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India.
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11
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Chen Q, Zobel J, Verspoor K. Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:baw163. [PMID: 28077566 PMCID: PMC5225397 DOI: 10.1093/database/baw163] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/22/2023]
Abstract
GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed. Existing duplicate detection methods in bioinformatics only address specific duplicate types, with inconsistent assumptions; and the impact of duplicates in bioinformatics databases has not been carefully assessed, making it difficult to judge the value of such methods. Our goal is to assess the scale, kinds and impact of duplicates in bioinformatics databases, through a retrospective analysis of merged groups in INSDC databases. Our outcomes are threefold: (1) We analyse a benchmark dataset consisting of duplicates manually identified in INSDC—a dataset of 67 888 merged groups with 111 823 duplicate pairs across 21 organisms from INSDC databases – in terms of the prevalence, types and impacts of duplicates. (2) We categorize duplicates at both sequence and annotation level, with supporting quantitative statistics, showing that different organisms have different prevalence of distinct kinds of duplicate. (3) We show that the presence of duplicates has practical impact via a simple case study on duplicates, in terms of GC content and melting temperature. We demonstrate that duplicates not only introduce redundancy, but can lead to inconsistent results for certain tasks. Our findings lead to a better understanding of the problem of duplication in biological databases. Database URL: the merged records are available at https://cloudstor.aarnet.edu.au/plus/index.php/s/Xef2fvsebBEAv9w
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Affiliation(s)
- Qingyu Chen
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Justin Zobel
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Karin Verspoor
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
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12
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Chen Q, Zobel J, Verspoor K. Benchmarks for measurement of duplicate detection methods in nucleotide databases. Database (Oxford) 2017; 2023:2870676. [PMID: 28334741 PMCID: PMC10755258 DOI: 10.1093/database/baw164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/01/2023]
Abstract
Duplication of information in databases is a major data quality challenge. The presence of duplicates, implying either redundancy or inconsistency, can have a range of impacts on the quality of analyses that use the data. To provide a sound basis for research on this issue in databases of nucleotide sequences, we have developed new, large-scale validated collections of duplicates, which can be used to test the effectiveness of duplicate detection methods. Previous collections were either designed primarily to test efficiency, or contained only a limited number of duplicates of limited kinds. To date, duplicate detection methods have been evaluated on separate, inconsistent benchmarks, leading to results that cannot be compared and, due to limitations of the benchmarks, of questionable generality. In this study, we present three nucleotide sequence database benchmarks, based on information drawn from a range of resources, including information derived from mapping to two data sections within the UniProt Knowledgebase (UniProtKB), UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. Each benchmark has distinct characteristics. We quantify these characteristics and argue for their complementary value in evaluation. The benchmarks collectively contain a vast number of validated biological duplicates; the largest has nearly half a billion duplicate pairs (although this is probably only a tiny fraction of the total that is present). They are also the first benchmarks targeting the primary nucleotide databases. The records include the 21 most heavily studied organisms in molecular biology research. Our quantitative analysis shows that duplicates in the different benchmarks, and in different organisms, have different characteristics. It is thus unreliable to evaluate duplicate detection methods against any single benchmark. For example, the benchmark derived from UniProtKB/Swiss-Prot mappings identifies more diverse types of duplicates, showing the importance of expert curation, but is limited to coding sequences. Overall, these benchmarks form a resource that we believe will be of great value for development and evaluation of the duplicate detection or record linkage methods that are required to help maintain these essential resources. DATABASE URL : https://bitbucket.org/biodbqual/benchmarks.
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Affiliation(s)
- Qingyu Chen
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Justin Zobel
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Karin Verspoor
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC 3010, Australia
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Saini A, Mahajan S, Gupta P. Nuclear receptor expression atlas in BMDCs: Nr4a2 restricts immunogenicity of BMDCs and impedes EAE. Eur J Immunol 2016; 46:1842-53. [PMID: 27184189 DOI: 10.1002/eji.201546229] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/19/2016] [Accepted: 05/12/2016] [Indexed: 01/25/2023]
Abstract
The nuclear receptor (NR) superfamily of transcription factors regulates various key aspects of physiological processes; however, their role(s) in immune cells' function are just beginning to unravel. Although few NRs have been shown to be critical for dendritic cell (DC) function, a lack of knowledge about their complete representation in DCs has limited the ability to harness their full potential. Here, we performed a comprehensive NR expression profiling and identified the key members of NR superfamily being expressed in immature, immunogenic, and tolerogenic DCs. Comparative analysis revealed discrete changes in the expression of various NRs among the studied DC subtypes, indicating a likely role in the modulation of DC functionality. Next, we characterized Nr4a2, a member of orphan NR family, and found that it suppresses the activation of bone marrow derived dendritic cells triggered by LPS. Overexpression and knockdown of Nr4a2 demonstrated that Nr4a2 orchestrates the expression of immunoregulatory genes, hence inducing a tolerogenic phenotype in bone marrow derived dendritic cells. Furthermore, we also found that Nr4a2 provides protection from EAE by promoting an increase in Treg cells, while limiting effector T cells. Our findings suggest a previously unidentified role for Nr4a2 as a regulator of DC tolerogenicity and demonstrate its potential as therapeutic target in DC-associated pathophysiologies.
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Affiliation(s)
- Ankita Saini
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India
| | - Sahil Mahajan
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India.,Department of Orthopedics, Washington University School of Medicine, St. Louis, MO, USA
| | - Pawan Gupta
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, 160036, India
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