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Young CH, Snow B, DeVore SB, Mohandass A, Nemmara VV, Thompson PR, Thyagarajan B, Navratil AM, Cherrington BD. Progesterone stimulates histone citrullination to increase IGFBP1 expression in uterine cells. Reproduction 2021; 162:117-127. [PMID: 34034233 PMCID: PMC8284904 DOI: 10.1530/rep-21-0132] [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: 03/25/2021] [Accepted: 05/25/2021] [Indexed: 12/31/2022]
Abstract
Peptidylarginine deiminases (PAD) enzymes were initially characterized in uteri, but since then little research has examined their function in this tissue. PADs post-translationally convert arginine residues in target proteins to citrulline and are highly expressed in ovine caruncle epithelia and ovine uterine luminal epithelial (OLE)-derived cell line. Progesterone (P4) not only maintains the uterine epithelia but also regulates the expression of endometrial genes that code for proteins that comprise the histotroph and are critical during early pregnancy. Given this, we tested whether P4 stimulates PAD-catalyzed histone citrullination to epigenetically regulate expression of the histotroph gene insulin-like growth factor binding protein 1 (IGFBP1) in OLE cells. 100 nM P4 significantly increases IGFBP1 mRNA expression; however, this increase is attenuated by pre-treating OLE cells with 100 nM progesterone receptor antagonist RU486 or 2 µM of a pan-PAD inhibitor. P4 treatment of OLE cells also stimulates citrullination of histone H3 arginine residues 2, 8, and 17 leading to enrichment of the ovine IGFBP1 gene promoter. Since PAD2 nuclear translocation and catalytic activity require calcium, we next investigated whether P4 triggers calcium influx in OLE cells. OLE cells were pre-treated with 10 nM nicardipine, an L-type calcium channel blocker, followed by stimulation with P4. Using fura2-AM imaging, we found that P4 initiates a rapid calcium influx through L-type calcium channels in OLE cells. Furthermore, this influx is necessary for PAD2 nuclear translocation and resulting citrullination of histone H3 arginine residues 2, 8, and 17. Our work suggests that P4 stimulates rapid calcium influx through L-type calcium channels initiating PAD-catalyzed histone citrullination and an increase in IGFBP1 expression.
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Affiliation(s)
- Coleman H Young
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Bryce Snow
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Stanley B DeVore
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Venkatesh V Nemmara
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Amy M Navratil
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Brian D Cherrington
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
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Cantonero C, Salido GM, Rosado JA, Redondo PC. PGRMC1 Inhibits Progesterone-Evoked Proliferation and Ca 2+ Entry Via STIM2 in MDA-MB-231 Cells. Int J Mol Sci 2020; 21:ijms21207641. [PMID: 33076541 PMCID: PMC7589959 DOI: 10.3390/ijms21207641] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Progesterone receptor membrane component 1 (PGRMC1) has been shown to regulate some cancer hallmarks. Progesterone (P4) evokes intracellular calcium (Ca2+) changes in the triple-negative breast cancer cell lines (MDA-MB-231, MDA-MB-468, and BT-20) and in other breast cancer cell lines like the luminal MCF7 cells. PGRMC1 expression is elevated in MDA-MB-231 and MCF7 cells as compared to non-tumoral MCF10A cell line, and PGRMC1 silencing enhances P4-evoked Ca2+ mobilization. Here, we found a new P4-dependent Ca2+ mobilization pathway in MDA-MB-231 cells and other triple-negative breast cancer cells, as well as in MCF7 cells that involved Stromal interaction molecule 2 (STIM2), Calcium release-activated calcium channel protein 1 (Orai1), and Transient Receptor Potential Channel 1 (TRPC1). Stromal interaction molecule 1 (STIM1) was not involved in this novel Ca2+ pathway, as evidenced by using siRNA STIM1. PGRMC1 silencing reduced the negative effect of P4 on cell proliferation and cell death in MDA-MB-231 cells. In line with the latter observation, Nuclear Factor of Activated T-Cells 1 (NFAT1) nuclear accumulation due to P4 incubation for 48 h was enhanced in cells transfected with the small hairpin siRNA against PGRMC1 (shPGRMC1). These results provide evidence for a novel P4-evoked Ca2+ entry pathway that is downregulated by PGRMC1.
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Azeez JM, Vini R, Remadevi V, Surendran A, Jaleel A, Santhosh Kumar TR, Sreeja S. VDAC1 and SERCA3 Mediate Progesterone-Triggered Ca2+ Signaling in Breast Cancer Cells. J Proteome Res 2017; 17:698-709. [DOI: 10.1021/acs.jproteome.7b00754] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Juberiya M. Azeez
- Cancer
Research Program and ‡Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Ravindran Vini
- Cancer
Research Program and ‡Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Viji Remadevi
- Cancer
Research Program and ‡Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Arun Surendran
- Cancer
Research Program and ‡Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Abdul Jaleel
- Cancer
Research Program and ‡Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - T. R. Santhosh Kumar
- Cancer
Research Program and ‡Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - S. Sreeja
- Cancer
Research Program and ‡Proteomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
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Sá SI, Fonseca BM. Dynamics of progesterone and estrogen receptor alpha in the ventromedial hypothalamus. J Endocrinol 2017; 233:197-207. [PMID: 28283583 DOI: 10.1530/joe-16-0663] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/10/2017] [Indexed: 12/28/2022]
Abstract
Cyclic fluctuations of estradiol and progesterone in females influence neuronal activity in the ventrolateral division of the ventromedial hypothalamic nucleus (VMNvl), through the activation of progesterone receptors (PRs) and estrogen receptors (ERs). The expression of ER and PR in the VMNvl is influenced by their cognate ligands and is a central upstream trigger in the pathway of VMNvl-dependent modulation of endocrine responses. By studying the role played by estradiol and progesterone in PR and ERa expression in the VMNvl along the estrous cycle and how the two receptors interact in the same neuron, we aim to evaluate the synergistic action of both ovarian hormones in the regulation of VMNvl activity. In animals at all phases of the estrous cycle, the number of VMN neurons expressing PR or ERa was estimated by stereological methods, and the percentage, and rostro-caudal distribution, of neurons simultaneously expressing both receptors was determined. The highest number of PR-immunoreactive neurons was seen at proestrus, and of ERa-immunoreactive neurons was seen at proestrus and metestrus. The ERa/PR co-localization is increased at caudal levels. Approximately half the neurons expressing PR co-express ERa, a proportion that stays constant along the estrous cycle. The percentage of ERa neurons co-expressing PR changes from 60% at proestrus to 40% at metestrus. Fluctuations in circulating ovarian hormone levels promote coordinated changes in PR and ERa expression and co-localization. This may be an important mechanism in the regulation of input relayed by the VMNvl, allowing a precise modulation of endocrine responses.
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Affiliation(s)
- Susana I Sá
- Department of BiomedicineUnit of Anatomy, Faculty of Medicine, University of Porto, Porto, Portugal
- Faculty of MedicineCenter for Health Technology and Services Research (CINTESIS), University of Porto, Porto, Portugal
| | - Bruno M Fonseca
- UCIBIOREQUIMTE, Department of Biological Sciences, Laboratory of Biochemistry, Faculty of Pharmacy, University of Porto, Porto, Portugal
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Chang HT, Chou CT, Chen IS, Yu CC, Lu T, Hsu SS, Shieh P, Jan CR, Liang WZ. Mechanisms underlying effect of the mycotoxin cytochalasin B on induction of cytotoxicity, modulation of cell cycle, Ca 2+ homeostasis and ROS production in human breast cells. Toxicology 2016; 370:1-19. [PMID: 27640744 DOI: 10.1016/j.tox.2016.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 01/04/2023]
Abstract
Cytochalasin B, a cell-permeable mycotoxin isolated from the fungus Phoma spp., shows a wide range of biological effects, among which its potent antitumor activity has raised great interests in different models. However, the cytotoxic activity of cytochalasin B and its underlying mechanisms have not been elucidated in breast cells. This study examined the effect of cytochalasin B on MCF 10A human breast epithelial cells and ZR-75-1 human breast cancer cells. Cytochalasin B (10-20μM) concentration-dependently induced cytotoxicity, cell cycle arrest, and [Ca2+]i rises in ZR-75-1 cells but not in MCF 10A cells. In ZR-75-1 cells, cytochalasin B triggered G2/M phase arrest through the modulation of CDK1, cyclin B1, p53, p27 and p21 expressions. The Ca2+ signal response induced by cytochalasin B was reduced by removing extracellular Ca2+ and was inhibited by the store-operated Ca2+ channel blocker 2-APB and SKF96365. In Ca2+-free medium, cytochalasin B induced Ca2+ release through thapsigargin-sensitive endoplasmic reticulum stores. Moreover, cytochalasin B increased H2O2 levels but reduced GSH levels. The apoptotic effects evoked by cytochalasin B were partially inhibited by prechelating cytosolic Ca2+ with BAPTA-AM and the antioxidant NAC. Together, in ZR-75-1 cells but not in MCF 10A cells, cytochalasin B activated Ca2+-associated mitochondrial apoptotic pathways that involved G2/M phase arrest and ROS signaling. Furthermore, cytochalasin B induced [Ca2+]i rises by releasing Ca2+ from the endoplasmic reticulum and causing Ca2+ influx through 2-APB or SKF96365-sensitive store-operated Ca2+ entry. Our findings provide new insights into the possible application of cytochalasin B in human breast cancer therapy.
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Affiliation(s)
- Hong-Tai Chang
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, ROC
| | - Chiang-Ting Chou
- Department of Nursing, Division of Basic Medical Sciences, Chang Gung University of Science and Technology, Chia-Yi 613, Taiwan, ROC; Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chia-Yi 613, Taiwan, ROC
| | - I-Shu Chen
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, ROC
| | - Chia-Cheng Yu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, ROC
| | - Ti Lu
- Department of Psychiatry, Kaohsiung Veterans General Hospital, Kaohsiung, 813, Taiwan, ROC
| | - Shu-Shong Hsu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, ROC
| | - Pochuen Shieh
- Department of Pharmacy, Tajen University, Pingtung 907, Taiwan, ROC
| | - Chung-Ren Jan
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, ROC
| | - Wei-Zhe Liang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, ROC,.
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Esculetin, a natural coumarin compound, evokes Ca2+ movement and activation of Ca2+-associated mitochondrial apoptotic pathways that involved cell cycle arrest in ZR-75-1 human breast cancer cells. Tumour Biol 2015; 37:4665-78. [DOI: 10.1007/s13277-015-4286-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/19/2015] [Indexed: 11/24/2022] Open
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Patel B, Elguero S, Thakore S, Dahoud W, Bedaiwy M, Mesiano S. Role of nuclear progesterone receptor isoforms in uterine pathophysiology. Hum Reprod Update 2014; 21:155-73. [PMID: 25406186 DOI: 10.1093/humupd/dmu056] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Progesterone is a key hormonal regulator of the female reproductive system. It plays a major role to prepare the uterus for implantation and in the establishment and maintenance of pregnancy. Actions of progesterone on the uterine tissues (endometrium, myometrium and cervix) are mediated by the combined effects of two progesterone receptor (PR) isoforms, designated PR-A and PR-B. Both receptors function primarily as ligand-activated transcription factors. Progesterone action on the uterine tissues is qualitatively and quantitatively determined by the relative levels and transcriptional activities of PR-A and PR-B. The transcriptional activity of the PR isoforms is affected by specific transcriptional coregulators and by PR post-translational modifications that affect gene promoter targeting. In this context, appropriate temporal and cell-specific expression and function of PR-A and PR-B are critical for normal uterine function. METHODS Relevant studies describing the role of PRs in uterine physiology and pathology (endometriosis, uterine leiomyoma, endometrial cancer, cervical cancer and recurrent pregnancy loss) were comprehensively searched using PubMed, Cochrane Library, Web of Science, and Google Scholar and critically reviewed. RESULTS Progesterone, acting through PR-A and PR-B, regulates the development and function of the endometrium and induces changes in cells essential for implantation and the establishment and maintenance of pregnancy. During pregnancy, progesterone via the PRs promotes myometrial relaxation and cervical closure. Withdrawal of PR-mediated progesterone signaling triggers menstruation and parturition. PR-mediated progesterone signaling is anti-mitogenic in endometrial epithelial cells, and as such, mitigates the tropic effects of estrogen on eutopic normal endometrium, and on ectopic implants in endometriosis. Similarly, ligand-activated PRs function as tumor suppressors in endometrial cancer cells through inhibition of key cellular signaling pathways required for growth. In contrast, progesterone via PR activation appears to increase leiomyoma growth. The exact role of PRs in cervical cancer is unclear. PRs regulate implantation and therefore aberrant PR function may be implicated in recurrent pregnancy loss (RPL). PRs likely regulate key immunogenic factors involved in RPL. However, the exact role of PRs in the pathophysiology of RPL and the use of progesterone for therapeutic benefit remains uncertain. CONCLUSIONS PRs are key mediators of progesterone action in uterine tissues and are essential for normal uterine function. Aberrant PR function (due to abnormal expression and/or function) is a major cause of uterine pathophysiology. Further investigation of the underlying mechanisms of PR isoform action in the uterus is required, as this knowledge will afford the opportunity to create progestin/PR-based therapeutics to treat various uterine pathologies.
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Affiliation(s)
- Bansari Patel
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sonia Elguero
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Suruchi Thakore
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Wissam Dahoud
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mohamed Bedaiwy
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Sam Mesiano
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Case Western Reserve University, Cleveland, OH 44106, USA
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Burnstock G, Di Virgilio F. Purinergic signalling and cancer. Purinergic Signal 2014; 9:491-540. [PMID: 23797685 DOI: 10.1007/s11302-013-9372-5] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/06/2013] [Indexed: 01/24/2023] Open
Abstract
Receptors for extracellular nucleotides are widely expressed by mammalian cells. They mediate a large array of responses ranging from growth stimulation to apoptosis, from chemotaxis to cell differentiation and from nociception to cytokine release, as well as neurotransmission. Pharma industry is involved in the development and clinical testing of drugs selectively targeting the different P1 nucleoside and P2 nucleotide receptor subtypes. As described in detail in the present review, P2 receptors are expressed by all tumours, in some cases to a very high level. Activation or inhibition of selected P2 receptor subtypes brings about cancer cell death or growth inhibition. The field has been largely neglected by current research in oncology, yet the evidence presented in this review, most of which is based on in vitro studies, although with a limited amount from in vivo experiments and human studies, warrants further efforts to explore the therapeutic potential of purinoceptor targeting in cancer.
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Sá SI, Pereira PA, Malikov V, Ferreira IM, Madeira MD. Role of plasma membrane estrogen receptors in mediating the estrogen induction of progesterone receptors in hypothalamic ventromedial neurons. J Comp Neurol 2013; 522:298-307. [DOI: 10.1002/cne.23396] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/22/2013] [Accepted: 06/19/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Susana I. Sá
- Department of Anatomy, Faculty of Medicine; University of Porto; 4200-319 Porto Portugal
| | - Pedro A. Pereira
- Department of Anatomy, Faculty of Medicine; University of Porto; 4200-319 Porto Portugal
| | - Viacheslav Malikov
- Department of Anatomy, Faculty of Medicine; University of Porto; 4200-319 Porto Portugal
| | - Isabel M.P.L.V.O. Ferreira
- REQUIMTE/Laboratory of Bromatology and Hidrology, Faculty of Pharmacy; University of Porto; 4050-313 Porto Portugal
| | - M. Dulce Madeira
- Department of Anatomy, Faculty of Medicine; University of Porto; 4200-319 Porto Portugal
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Sá S, Pereira P, Malikov V, Madeira M. Role of estrogen receptor α and β in the induction of progesterone receptors in hypothalamic ventromedial neurons. Neuroscience 2013; 238:159-67. [DOI: 10.1016/j.neuroscience.2013.02.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/14/2013] [Indexed: 10/27/2022]
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Jain R, Javidan-Nejad C, Alexander-Brett J, Horani A, Cabellon MC, Walter MJ, Brody SL. Sensory functions of motile cilia and implication for bronchiectasis. Front Biosci (Schol Ed) 2012; 4:1088-98. [PMID: 22202111 DOI: 10.2741/s320] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cilia are specialized organelles that extend from the cell surface into the local environment. Cilia of the airway epithelia are motile to provide mucociliary clearance. On other cells, solitary cilia are specialized to detect chemical or mechanosensory signals. Sensory proteins in motile cilia have recently been identified that detect fluid flow, bitter taste and sex hormones. The relationship of these sensory functions in motile cilia to disease is now being revealed. An example are the polycystin-1 and polycystin-2 proteins that function as a flow sensor in kidney cilia and are mutated in autosomal dominant polycystic kidney disease (ADPKD). These polycystins are also expressed in motile cilia, potentially operating as sensors in the lung. Computed tomography studies from patients with ADPKD reveal evidence of bronchiectasis, suggesting polycystins are important in lung function. The motile cilia expression of this protein complex, as well as sensory channel TRPV4, bitter taste and sex hormones receptors, indicate that the cilia is wired to interpret environmental cues. Defective signaling of sensory proteins may result in a ciliopathy that includes lung disease.
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Affiliation(s)
- Raksha Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
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Interaction of purinergic receptors with GPCRs, ion channels, tyrosine kinase and steroid hormone receptors orchestrates cell function. Purinergic Signal 2011; 8:91-103. [PMID: 21887492 DOI: 10.1007/s11302-011-9260-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 08/16/2011] [Indexed: 01/26/2023] Open
Abstract
Extracellular purines and pyrimidines have emerged as key regulators of a wide range of physiological and pathophysiological cellular processes acting through P1 and P2 cell surface receptors. Increasing evidence suggests that purinergic receptors can interact with and/or modulate the activity of other classes of receptors and ion channels. This review will focus on the interactions of purinergic receptors with other GPCRs, ion channels, receptor tyrosine kinases, and steroid hormone receptors. Also, the signal transduction pathways regulated by these complexes and their new functional properties are discussed.
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Arrais JP, Fernandes J, Pereira J, Oliveira JL. GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. BMC Bioinformatics 2010; 11:389. [PMID: 20663121 PMCID: PMC2919517 DOI: 10.1186/1471-2105-11-389] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relevant biological roles for the problem at hand. The required information is typically available in public databases, and usually, this information must be manually retrieved to complement the analysis. This process is a very time-consuming task that should be automated as much as possible. RESULTS GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways. CONCLUSIONS GeneBrowser provides a unique entry point to several visualisation and analysis methods, providing fast and easy analysis of a set of genes. GeneBrowser fills the gap between Web portals that analyse one gene at a time and functional analysis tools that are limited in scope and usually desktop-based.
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Affiliation(s)
- Joel P Arrais
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal
| | - João Fernandes
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal
| | - João Pereira
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal
| | - José Luís Oliveira
- Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, 3810-193 Aveiro, Portugal
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