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Najm M, Cornet M, Albergante L, Zinovyev A, Sermet-Gaudelus I, Stoven V, Calzone L, Martignetti L. Representation and quantification of module activity from omics data with rROMA. NPJ Syst Biol Appl 2024; 10:8. [PMID: 38242871 PMCID: PMC10799004 DOI: 10.1038/s41540-024-00331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
The efficiency of analyzing high-throughput data in systems biology has been demonstrated in numerous studies, where molecular data, such as transcriptomics and proteomics, offers great opportunities for understanding the complexity of biological processes. One important aspect of data analysis in systems biology is the shift from a reductionist approach that focuses on individual components to a more integrative perspective that considers the system as a whole, where the emphasis shifted from differential expression of individual genes to determining the activity of gene sets. Here, we present the rROMA software package for fast and accurate computation of the activity of gene sets with coordinated expression. The rROMA package incorporates significant improvements in the calculation algorithm, along with the implementation of several functions for statistical analysis and visualizing results. These additions greatly expand the package's capabilities and offer valuable tools for data analysis and interpretation. It is an open-source package available on github at: www.github.com/sysbio-curie/rROMA . Based on publicly available transcriptomic datasets, we applied rROMA to cystic fibrosis, highlighting biological mechanisms potentially involved in the establishment and progression of the disease and the associated genes. Results indicate that rROMA can detect disease-related active signaling pathways using transcriptomic and proteomic data. The results notably identified a significant mechanism relevant to cystic fibrosis, raised awareness of a possible bias related to cell culture, and uncovered an intriguing gene that warrants further investigation.
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Affiliation(s)
- Matthieu Najm
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Matthieu Cornet
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Luca Albergante
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Andrei Zinovyev
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Isabelle Sermet-Gaudelus
- Faculté de Médecine, Université de Paris, Paris, France
- Institut Necker Enfants Malades, INSERM U1151, Paris, France
- AP-HP. Centre - Université Paris Cité; Hôpital Necker Enfants Malades, Centre de Référence Maladie Rare - Mucoviscidose, Paris, France
| | - Véronique Stoven
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Laurence Calzone
- INSERM U900, 75428, Paris, France
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France
- Institut Curie, PSL Research University, 75248, Paris, France
| | - Loredana Martignetti
- INSERM U900, 75428, Paris, France.
- Center for Computational Biology, Mines ParisTech, PSL Research University, 75006, Paris, France.
- Institut Curie, PSL Research University, 75248, Paris, France.
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Quaresma MC, Botelho HM, Pankonien I, Rodrigues CS, Pinto MC, Costa PR, Duarte A, Amaral MD. Exploring YAP1-centered networks linking dysfunctional CFTR to epithelial-mesenchymal transition. Life Sci Alliance 2022; 5:5/9/e202101326. [PMID: 35500936 PMCID: PMC9060002 DOI: 10.26508/lsa.202101326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 12/21/2022] Open
Abstract
In this work, a systems biology approach identifies potentially dysregulated EMT signaling in CF (including the Hippo, Wnt, TGF-β, p53, and MYC pathways), integrated by YAP1 and TEAD4. Mutations in the CFTR anion channel cause cystic fibrosis (CF) and have also been related to higher cancer incidence. Previously we proposed that this is linked to an emerging role of functional CFTR in protecting against epithelial–mesenchymal transition (EMT). However, the pathways bridging dysfunctional CFTR to EMT remain elusive. Here, we applied systems biology to address this question. Our data show that YAP1 is aberrantly active in the presence of mutant CFTR, interacting with F508del, but not with wt-CFTR, and that YAP1 knockdown rescues F508del-CFTR processing and function. Subsequent analysis of YAP1 interactors and roles in cells expressing either wt- or F508del-CFTR reveal that YAP1 is an important mediator of the fibrotic/EMT processes in CF. Alongside, five main pathways emerge here as key in linking mutant CFTR to EMT, namely, (1) the Hippo pathway; (2) the Wnt pathway; (3) the TGFβ pathway; (4) the p53 pathway; and (5) MYC signaling. Several potential hub proteins which mediate the crosstalk among these pathways were also identified, appearing as potential therapeutic targets for both CF and cancer.
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Affiliation(s)
- Margarida C Quaresma
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Hugo M Botelho
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Ines Pankonien
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Cláudia S Rodrigues
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Madalena C Pinto
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Pau R Costa
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Aires Duarte
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Margarida D Amaral
- BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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3
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AHR Signaling Dampens Inflammatory Signature in Neonatal Skin γδ T Cells. Int J Mol Sci 2020; 21:ijms21062249. [PMID: 32213963 PMCID: PMC7139545 DOI: 10.3390/ijms21062249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/16/2022] Open
Abstract
Background Aryl hydrocarbon receptor (AHR)-deficient mice do not support the expansion of dendritic epidermal T cells (DETC), a resident immune cell population in the murine epidermis, which immigrates from the fetal thymus to the skin around birth. Material and Methods In order to identify the gene expression changes underlying the DETC disappearance in AHR-deficient mice, we analyzed microarray RNA-profiles of DETC, sorted from the skin of two-week-old AHR-deficient mice and their heterozygous littermates. In vitro studies were done for verification, and IL-10, AHR repressor (AHRR), and c-Kit deficient mice analyzed for DETC frequency. Results We identified 434 annotated differentially expressed genes. Gene set enrichment analysis demonstrated that the expression of genes related to proliferation, ion homeostasis and morphology differed between the two mouse genotypes. Importantly, with 1767 pathways the cluster-group “inflammation” contained the majority of AHR-dependently regulated pathways. The most abundant cluster of differentially expressed genes was “inflammation.” DETC of AHR-deficient mice were inflammatory active and had altered calcium and F-actin levels. Extending the study to the AHRR, an enigmatic modulator of AHR-activity, we found approximately 50% less DETC in AHRR-deficient mice than in wild-type-littermates. Conclusion AHR-signaling in DETC dampens their inflammatory default potential and supports their homeostasis in the skin.
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Palma AG, Galizia L, Kotsias BA, Marino GI. CFTR channel in oocytes from Xenopus laevis and its regulation by xShroom1 protein. Pflugers Arch 2016; 468:871-80. [PMID: 26888038 DOI: 10.1007/s00424-016-1800-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 02/10/2016] [Indexed: 01/24/2023]
Abstract
Shroom is a family of related proteins linked to the actin cytoskeleton. xShroom1 is constitutively expressed in Xenopus laevis oocytes, and it is required for the expression of the epithelial sodium channel (ENaC). As there is a close relationship between ENaC and the cystic fibrosis transmembrane regulator (CFTR), we examined the action of xShroom1 on CFTR expression and activity. Biotinylation was used to measure CFTR surface expression, and currents were registered with voltage clamp when stimulated with forskolin and 3-isobutyl-1-methylxanthine. Oocytes were coinjected with CFTR complementary RNAs (cRNAs) and xShroom1 sense or antisense oligonucleotides. We observed an increment in CFTR currents and CFTR surface expression in oocytes coinjected with CFTR and xShroom1 antisense oligonucleotides. MG-132, a proteasome inhibitor, did not prevent the increment in currents when xShroom1 was suppressed by antisense oligonucleotides. In addition, we inhibited the delivery of newly synthesized proteins to the plasma membrane with BFA and we found that the half-life of plasma membrane CFTR was prolonged when coinjected with the xShroom1 antisense oligonucleotides. Chloroquine, an inhibitor of the late endosome/lysosome, did not significantly increase CFTR currents when xShroom1 expression was inhibited. The higher expression of CFTR when xShroom1 is suppressed is in concordance with the functional studies suggesting that the suppression of the xShroom1 protein resulted in an increment in CFTR currents by promoting the increase of the half-life of CFTR in the plasma membrane. The role of xShroom1 in regulating CFTR expression could be relevant in the understanding of the channel malfunction in several diseases.
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Affiliation(s)
- Alejandra G Palma
- Laboratorio de Canales Iónicos, Instituto de Investigaciones Médicas Alfredo Lanari, Universidad de Buenos Aires, IDIM-CONICET, C. de Malvinas 3150, 1427, Buenos Aires, Argentina
| | - Luciano Galizia
- Laboratorio de Canales Iónicos, Instituto de Investigaciones Médicas Alfredo Lanari, Universidad de Buenos Aires, IDIM-CONICET, C. de Malvinas 3150, 1427, Buenos Aires, Argentina
| | - Basilio A Kotsias
- Laboratorio de Canales Iónicos, Instituto de Investigaciones Médicas Alfredo Lanari, Universidad de Buenos Aires, IDIM-CONICET, C. de Malvinas 3150, 1427, Buenos Aires, Argentina
| | - Gabriela I Marino
- Laboratorio de Canales Iónicos, Instituto de Investigaciones Médicas Alfredo Lanari, Universidad de Buenos Aires, IDIM-CONICET, C. de Malvinas 3150, 1427, Buenos Aires, Argentina.
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Burow P, Klapperstück M, Markwardt F. Activation of ATP secretion via volume-regulated anion channels by sphingosine-1-phosphate in RAW macrophages. Pflugers Arch 2014; 467:1215-26. [PMID: 24965069 DOI: 10.1007/s00424-014-1561-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/17/2014] [Indexed: 12/13/2022]
Abstract
We report the activation of outwardly rectifying anion currents by sphingosine-1-phosphate (S1P) in the murine macrophage cell line RAW 264.7. The S1P-induced current is mainly carried by anions, because the reversal potential of the current was shifted by replacement of extracellular Cl(-) by glutamate(-) but not when extracellular Na(+) was substituted by Tris(+). The inhibition of the current by hypertonic extracellular or hypotonic intracellular solution as well as the inhibitory effects of NPPB, tamoxifen, and glibenclamide indicates that the anion current is mediated by volume-regulated anion channels (VRAC). The S1P effect was blocked by intracellular GDPβS and W123, which points to signaling via the S1P receptor 1 (S1PR1) and G proteins. As cytochalasin D diminished the action of S1P, we conclude that the actin cytoskeleton is involved in the stimulation of VRAC. S1P and hypotonic extracellular solution induced secretion of ATP from the macrophages, which in both cases was blocked in a similar way by typical VRAC blockers. We suppose that the S1P-induced ATP secretion in macrophages via activation of VRAC constitutes a functional link between sphingolipid and purinergic signaling in essential processes such as inflammation and migration of leukocytes as well as phagocytosis and the killing of intracellular bacteria.
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Affiliation(s)
- Philipp Burow
- Julius Bernstein Institute for Physiology, Martin Luther University Halle, Magdeburger Str. 6, 06097, Halle/Saale, Germany
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Frizzell RA, Hanrahan JW. Physiology of epithelial chloride and fluid secretion. Cold Spring Harb Perspect Med 2013; 2:a009563. [PMID: 22675668 DOI: 10.1101/cshperspect.a009563] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epithelial salt and water secretion serves a variety of functions in different organ systems, such as the airways, intestines, pancreas, and salivary glands. In cystic fibrosis (CF), the volume and/or composition of secreted luminal fluids are compromised owing to mutations in the gene encoding CFTR, the apical membrane anion channel that is responsible for salt secretion in response to cAMP/PKA stimulation. This article examines CFTR and related cellular transport processes that underlie epithelial anion and fluid secretion, their regulation, and how these processes are altered in CF disease to account for organ-specific secretory phenotypes.
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Affiliation(s)
- Raymond A Frizzell
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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Mondini A, Sassone F, Civello DA, Garavaglia ML, Bazzini C, Rodighiero S, Vezzoli V, Conti F, Torielli L, Capasso G, Paulmichl M, Meyer G. Hypertension-linked mutation of α-adducin increases CFTR surface expression and activity in HEK and cultured rat distal convoluted tubule cells. PLoS One 2012; 7:e52014. [PMID: 23284854 PMCID: PMC3528715 DOI: 10.1371/journal.pone.0052014] [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: 05/22/2012] [Accepted: 11/08/2012] [Indexed: 11/18/2022] Open
Abstract
The CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) activity and localization are influenced by the cytoskeleton, in particular by actin and its polymerization state. In this study we investigated whether the expression of the hypertensive mutations of α-adducin (G460W-S586C in humans, F316Y in rats), an actin capping protein, led to a functional modification of CFTR activity and surface expression. The experiments were performed on HEK293 T cells cotransfected with CFTR and the human wild type (WT) or G460W mutated α-adducin. In whole-cell patch-clamp experiments, both the CFTR chloride current and the slope of current activation after forskolin addition were significantly higher in HEK cells overexpressing the G460W adducin. A higher plasma membrane density of active CFTR channels was confirmed by cell-attached patch-clamp experiments, both in HEK cells and in cultured primary DCT cells, isolated from MHS (Milan Hypertensive Strain, a Wistar rat (Rattus norvegicus) hypertensive model carrying the F316Y adducin mutation), compared to MNS (Milan Normotensive Strain) rats. Western blot experiments demonstrated an increase of the plasma membrane CFTR protein expression, with a modification of the channel glycosylation state, in the presence of the mutated adducin. A higher retention of CFTR protein in the plasma membrane was confirmed both by FRAP (Fluorescence Recovery After Photobleaching) and photoactivation experiments. The present data indicate that in HEK cells and in isolated DCT cells the presence of the G460W-S586C hypertensive variant of adducin increases CFTR channel activity, possibly by altering its membrane turnover and inducing a retention of the channel in the plasmamembrane. Since CFTR is known to modulate the activity of many others transport systems, the increased surface expression of the channel could have consequences on the whole network of transport in kidney cells.
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Affiliation(s)
- Anna Mondini
- Department of Life Sciences, Università degli Studi di Milano, Milano, Italy
| | - Francesca Sassone
- Department of Life Sciences, Università degli Studi di Milano, Milano, Italy
| | | | | | - Claudia Bazzini
- Department of Life Sciences, Università degli Studi di Milano, Milano, Italy
| | | | - Valeria Vezzoli
- Department of Life Sciences, Università degli Studi di Milano, Milano, Italy
| | - Fabio Conti
- Prassis Research Institute, Sigma Tau, Settimo M.se, Italy
| | - Lucia Torielli
- Prassis Research Institute, Sigma Tau, Settimo M.se, Italy
| | | | - Markus Paulmichl
- Institut of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Giuliano Meyer
- Department of Life Sciences, Università degli Studi di Milano, Milano, Italy
- * E-mail:
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Duan Y, Sun Y, Zhang F, Zhang WK, Wang D, Wang Y, Cao X, Hu W, Xie C, Cuppoletti J, Magin TM, Wang H, Wu Z, Li N, Huang P. Keratin K18 increases cystic fibrosis transmembrane conductance regulator (CFTR) surface expression by binding to its C-terminal hydrophobic patch. J Biol Chem 2012; 287:40547-59. [PMID: 23045527 DOI: 10.1074/jbc.m112.403584] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND CFTR function is tightly regulated by many interacting proteins. RESULTS Intermediate filament protein keratin 18 increases the cell surface expression of CFTR by interacting with the C-terminal hydrophobic patch of CFTR. CONCLUSION K18 controls the function of CFTR. SIGNIFICANCE These findings offer novel insights into the regulation of CFTR and suggest that K18 and its dimerization partner, K8, may be modifier genes in cystic fibrosis. Malfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) leads to cystic fibrosis, but the regulation of CFTR is not fully understood. Here, we identified the intermediate filament protein keratin K18 (K18) as a CFTR-binding protein by various approaches. We mapped a highly conserved "hydrophobic patch" ((1413)FLVI(1416)) in the CFTR C-terminus, known to determine plasmalemmal CFTR stability, as the K18-binding site. On the other hand, the C-terminal tail of K18 was found to be a critical determinant for binding CFTR. Overexpression of K18 in cells robustly increased the surface expression of wild-type CFTR, whereas depletion of K18 through RNA interference specifically diminished it. K18 binding increased the surface expression of CFTR by accelerating its apical recycling rate without altering CFTR biosynthesis, maturation, or internalization. Importantly, CFTR surface expression was markedly reduced in duodenal and gallbladder epithelia of K18(-/-) mice. Taken together, our results suggest that K18 increases the cell surface expression of CFTR by interacting with the CFTR C-terminal hydrophobic patch. These findings offer novel insights into the regulation of CFTR and suggest that K18 and its dimerization partner, K8, may be modifier genes in cystic fibrosis.
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Affiliation(s)
- Yuanyuan Duan
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
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Monterisi S, Favia M, Guerra L, Cardone RA, Marzulli D, Reshkin SJ, Casavola V, Zaccolo M. CFTR regulation in human airway epithelial cells requires integrity of the actin cytoskeleton and compartmentalized cAMP and PKA activity. J Cell Sci 2012; 125:1106-17. [PMID: 22302988 DOI: 10.1242/jcs.089086] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) mutation ΔF508CFTR still causes regulatory defects when rescued to the apical membrane, suggesting that the intracellular milieu might affect its ability to respond to cAMP regulation. We recently reported that overexpression of the Na(+)/H(+) exchanger regulatory factor NHERF1 in the cystic fibrosis (CF) airway cell line CFBE41o-rescues the functional expression of ΔF508CFTR by promoting F-actin organization and formation of the NHERF1-ezrin-actin complex. Here, using real-time FRET reporters of both PKA activity and cAMP levels, we find that lack of an organized subcortical cytoskeleton in CFBE41o-cells causes both defective accumulation of cAMP in the subcortical compartment and excessive cytosolic accumulation of cAMP. This results in reduced subcortical levels and increased cytosolic levels of PKA activity. NHERF1 overexpression in CFBE41o-cells restores chloride secretion, subcortical cAMP compartmentalization and local PKA activity, indicating that regulation of ΔF508CFTR function requires not only stable expression of the mutant CFTR at the cell surface but also depends on both generation of local cAMP signals of adequate amplitude and activation of PKA in proximity of its target. Moreover, we found that the knockdown of wild-type CFTR in the non-CF 16HBE14o-cells results in both altered cytoskeletal organization and loss of cAMP compartmentalization, whereas stable overexpression of wt CFTR in CF cells restores cytoskeleton organization and re-establishes the compartmentalization of cAMP at the plasma membrane. This suggests that the presence of CFTR on the plasma membrane influences the cytoskeletal organizational state and, consequently, cAMP distribution. Our data show that a sufficiently high concentration of cAMP in the subcortical compartment is required to achieve PKA-mediated regulation of CFTR activity.
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Affiliation(s)
- Stefania Monterisi
- Department of General and Environmental Physiology, University of Bari, Bari, 70125, Italy
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The plasma membrane potential and the organization of the actin cytoskeleton of epithelial cells. Int J Cell Biol 2012; 2012:121424. [PMID: 22315611 PMCID: PMC3272338 DOI: 10.1155/2012/121424] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 10/08/2011] [Indexed: 12/22/2022] Open
Abstract
The establishment and maintenance of the polarized epithelial phenotype require a characteristic organization of the cytoskeletal components. There are many cellular effectors involved in the regulation of the cytoskeleton of epithelial cells. Recently, modifications in the plasma membrane potential (PMP) have been suggested to participate in the modulation of the cytoskeletal organization of epithelia. Here, we review evidence showing that changes in the PMP of diverse epithelial cells promote characteristic modifications in the cytoskeletal organization, with a focus on the actin cytoskeleton. The molecular paths mediating these effects may include voltage-sensitive integral membrane proteins and/or peripheral proteins sensitive to surface potentials. The voltage dependence of the cytoskeletal organization seems to have implications in several physiological processes, including epithelial wound healing and apoptosis.
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l'Hoste S, Chargui A, Belfodil R, Corcelle E, Duranton C, Rubera I, Poujeol C, Mograbi B, Tauc M, Poujeol P. CFTR mediates apoptotic volume decrease and cell death by controlling glutathione efflux and ROS production in cultured mice proximal tubules. Am J Physiol Renal Physiol 2010; 298:F435-53. [DOI: 10.1152/ajprenal.00286.2009] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have previously shown that despite the presence of mRNA encoding CFTR, renal proximal cells do not exhibit cAMP-sensitive Cl−conductance (Rubera I, Tauc M, Bidet M, Poujeol C, Cuiller B, Watrin A, Touret N, Poujeol P. Am J Physiol Renal Physiol 275: F651–F663, 1998). Nevertheless, in these cells, CFTR plays a crucial role in the control of the volume-sensitive outwardly rectifying (VSOR) activated Cl−currents during hypotonic shock. The aim of this study was to determine the role of CFTR in the regulation of apoptosis volume decrease (AVD) and the apoptosis phenomenon. For this purpose, renal cells were immortalized from primary cultures of proximal convoluted tubules from cftr+/+and cftr−/−mice. Apoptosis was induced by staurosporine (STS; 1 μM). Cell volume, Cl−conductance, caspase-3 activity, intracellular level of reactive oxygen species (ROS), and glutathione content (GSH/GSSG) were monitored during AVD. In cftr+/+cells, AVD and caspase-3 activation were strongly impaired by conventional Cl−channel blockers and by a specific CFTR inhibitor (CFTRinh-172; 5 μM). STS induced activation of CFTR conductance within 15 min, which was progressively replaced by VSOR Cl−currents after 60 min of exposure. In parallel, STS induced an increase in ROS content in the time course of VSOR Cl−current activation. This increase was impaired by CFTRinh-172 and was not observed in cftr−/−cells. Furthermore, the intracellular GSH/GSSG content decreased during STS exposure in cftr+/+cells only. In conclusion, CFTR could play a key role in the cascade of events leading to apoptosis. This role probably involves control of the intracellular ROS balance by some CFTR-dependent modulation of GSH concentration.
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Affiliation(s)
| | | | | | | | | | | | | | - Baharia Mograbi
- Inflammation et Carcinogenese (INSERM ERI21) UFR Medecine, Nice, France
| | - Michel Tauc
- CNRS FRE 3093, Université de Nice-Sophia Antipolis, and
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Cohen JC, Killeen E, Chander A, Takemaru KI, Larson JE, Treharne KJ, Mehta A. Small interfering peptide (siP) for in vivo examination of the developing lung interactonome. Dev Dyn 2009; 238:386-93. [PMID: 19161244 PMCID: PMC2808203 DOI: 10.1002/dvdy.21834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
To understand the role of reactive oxygen species in mechanosensory control of lung development a new approach to interfere with protein-protein interactions by means of a short interacting peptide was developed. This technology was used in the developing rodent lung to examine the role of NADPH oxidase (NOX), casein kinase 2 (CK2), and the cystic fibrosis transmembrane conductance regulator (CFTR) in stretch-induced differentiation. Interactions between these molecules was targeted in an in utero system with recombinant adeno-associated virus (rAAV) containing inserted DNA sequences that express a control peptide or small interfering peptides (siPs) specific for subunit interaction or phosphorylation predicted to be necessary for multimeric enzyme formation. In all cases only siPs with sequences necessary for a predicted normal function were found to interfere with assembly of the multimeric enzyme. A noninterfering control siP to nonessential regions or reporter genes alone had no effect. Physiologically, it was shown that siPs that interfered with the NOX-CFTR-CK2 complex that we call an "interactonome" affected markers of stretch-induced lung organogenesis including Wnt/beta-catenin signaling.
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Affiliation(s)
- J Craig Cohen
- The Brady Laboratory, Section of Neonatology, Department of Pediatrics, Stony Brook University, School of Medicine, Stony Brook, New York 11794, USA.
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Cohen JC, Larson JE, Killeen E, Love D, Takemaru KI. CFTR and Wnt/beta-catenin signaling in lung development. BMC DEVELOPMENTAL BIOLOGY 2008; 8:70. [PMID: 18601749 PMCID: PMC2464600 DOI: 10.1186/1471-213x-8-70] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 07/06/2008] [Indexed: 01/16/2023]
Abstract
BACKGROUND Cystic fibrosis transmembrane conductance regulator (CFTR) was shown previously to modify stretch induced differentiation in the lung. The mechanism for CFTR modulation of lung development was examined by in utero gene transfer of either a sense or antisense construct to alter CFTR expression levels. The BAT-gal transgenic reporter mouse line, expressing beta-galactosidase under a canonical Wnt/beta-catenin-responsive promoter, was used to assess the relative roles of CFTR, Wnt, and parathyroid hormone-related peptide (PTHrP) in lung organogenesis. Adenoviruses containing full-length CFTR, a short anti-sense CFTR gene fragment, or a reporter gene as control were used in an intra-amniotic gene therapy procedure to transiently modify CFTR expression in the fetal lung. RESULTS A direct correlation between CFTR expression levels and PTHrP levels was found. An inverse correlation between CFTR and Wnt signaling activities was demonstrated. CONCLUSION These data are consistent with CFTR participating in the mechanicosensory process essential to regulate Wnt/beta-Catenin signaling required for lung organogenesis.
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Affiliation(s)
- J Craig Cohen
- The Brady Laboratory, Section of Neonatology, Department of Pediatrics, Stony Brook University, School of Medicine, Stony Brook, New York, USA.
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14
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Doering CJ, Rehak R, Bonfield S, Peloquin JB, Stell WK, Mema SC, Sauvé Y, McRory JE. Modified Ca(v)1.4 expression in the Cacna1f(nob2) mouse due to alternative splicing of an ETn inserted in exon 2. PLoS One 2008; 3:e2538. [PMID: 18596967 PMCID: PMC2432030 DOI: 10.1371/journal.pone.0002538] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 05/15/2008] [Indexed: 01/19/2023] Open
Abstract
The Cacna1fnob2 mouse is reported to be a naturally occurring null mutation for the Cav1.4 calcium channel gene and the phenotype of this mouse is not identical to that of the targeted gene knockout model. We found two mRNA species in the Cacna1fnob2 mouse: approximately 90% of the mRNA represents a transcript with an in-frame stop codon within exon 2 of CACNA1F, while approximately 10% of the mRNA represents a transcript in which alternative splicing within the ETn element has removed the stop codon. This latter mRNA codes for full length Cav1.4 protein, detectable by Western blot analysis that is predicted to differ from wild type Cav1.4 protein in a region of approximately 22 amino acids in the N-terminal portion of the protein. Electrophysiological analysis with either mouse Cav1.4wt or Cav1.4nob2 cDNA revealed that the alternatively spliced protein does not differ from wild type with respect to activation and inactivation characteristics; however, while the wild type N-terminus interacted with filamin proteins in a biochemical pull-down experiment, the alternatively spliced N-terminus did not. The Cacna1fnob2 mouse electroretinogram displayed reduced b-wave and oscillatory potential amplitudes, and the retina was morphologically disorganized, with substantial reduction in thickness of the outer plexiform layer and sprouting of bipolar cell dendrites ectopically into the outer nuclear layer. Nevertheless, the spatial contrast sensitivity (optokinetic response) of Cacna1fnob2 mice was generally similar to that of wild type mice. These results suggest the Cacna1fnob2 mouse is not a CACNA1F knockout model. Rather, alternative splicing within the ETn element can lead to full-length Cav1.4 protein, albeit at reduced levels, and the functional Cav1.4 mutant may be incapable of interacting with cytoskeletal filamin proteins. These changes, do not alter the ability of the Cacna1fnob2 mouse to detect and follow moving sine-wave gratings compared to their wild type counterparts.
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Affiliation(s)
- Clinton J. Doering
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - Renata Rehak
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Stephan Bonfield
- Cell Biology and Anatomy / Surgery, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - Jean B. Peloquin
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - William K. Stell
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Cell Biology and Anatomy / Surgery, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
| | - Silvina C. Mema
- Department of Ophthalmology, University of Alberta, Edmonton, Canada
| | - Yves Sauvé
- Department of Ophthalmology, University of Alberta, Edmonton, Canada
| | - John E. McRory
- Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
- Lions Centre for Retinal Degeneration Research, University of Calgary, Calgary, Canada
- * E-mail:
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15
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Swystun V, Chen L, Factor P, Siroky B, Bell PD, Matalon S. Apical trypsin increases ion transport and resistance by a phospholipase C-dependent rise of Ca2+. Am J Physiol Lung Cell Mol Physiol 2005; 288:L820-30. [PMID: 15626748 DOI: 10.1152/ajplung.00396.2004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We investigated the mechanisms by which serine proteases alter lung fluid clearance in rat lungs and vectorial ion transport in airway and alveolar epithelial cells. Inhibition of endogenous protease activity by intratracheal instillation of soybean trypsin inhibitor (SBTI) or α1-antitrypsin decreased amiloride-sensitive lung fluid clearance across rat fluid-filled lungs; instillation of trypsin partially restored this effect. Gelatin zymography demonstrated SBTI-inhibitable trypsin-like activity in rat lung lavage fluid. Apical trypsin and human neutrophil elastase, but not agonists of protease activated receptors, increased Na+and Cl−short-circuit currents ( Isc) and transepithelial resistance ( RTE) across human bronchial and nasal epithelial cells and rat alveolar type II cells, mounted in Ussing chambers, for at least 2 h. The increase in Iscwas fully reversed by amiloride and glibenclamide. The increase in RTEwas not prevented by ouabain, suggesting that trypsin decreased paracellular conductance. Apical trypsin also induced a transient increase in intracellular Ca2+in human airway cells; treatment of these cells with BAPTA-AM mitigated the trypsin-induced increases of intracellular Ca2+and of Iscand RTE. Increasing intracellular Ca2+in airway cells with either ionomycin or thapsigargin reproduced the increase in Isc, whereas inhibitors of phospholipase C (PLC) prevented the increases in both Ca2+and Isc. These data indicate trypsin-like proteases and elastase, either present in lung cells or released by inflammatory cells into the alveolar space, play an important role in the clearance of alveolar fluid by increasing ion transport and paracellular resistance via a PLC-initiated rise of intracellular Ca2+.
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Affiliation(s)
- Veronica Swystun
- University of Alabama at Birmingham, Dept. of Anesthesiology, AL 35205-3703, USA
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16
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Davezac N, Tondelier D, Lipecka J, Fanen P, Demaugre F, Debski J, Dadlez M, Schrattenholz A, Cahill MA, Edelman A. Global proteomic approach unmasks involvement of keratins 8 and 18 in the delivery of cystic fibrosis transmembrane conductance regulator (CFTR)/?F508-CFTR to the plasma membrane. Proteomics 2004; 4:3833-44. [PMID: 15529338 DOI: 10.1002/pmic.200400850] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations in the CF gene (cftr). Physiologically, CF is characterized by an abnormal chloride secretion in epithelia due to a dysfunction of a mutated cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is a cAMP-dependent chloride channel whose most frequent mutation, deltaF508, leads to an aberrantly folded protein which causes a dysfunction of the channel. However, a growing number of reports suggest that modifier genes and environmental factors are involved in the physiology of CF. To identify proteins whose expression depends on wild-type WT-CFTR or deltaF508-CFTR, we chose a global proteomic approach based on the use of two-dimensional gel electrophoresis (2-DE) and mass spectrometry. The experiments were carried out with HeLa cells stably transfected with WT-CFTR (pTCFWT) or deltaF508-CFTR (pTCFdeltaF508). These experiments unmasked keratin 8 (K8) and 18 (K18) which were differentially expressed in pTCFWT vs. pTCFdeltaF508. An immunoblot of K18 confirmed the 2-DE results. Intracellular localization experiments of WT-CFTR, deltaF508-CFTR, K8, and K18 suggest that the expression of these proteins are linked, and that the concentrations of K8 and K18 and/or their distribution may be involved in the traffic of WT-CFTR/deltaF508-CFTR. A functional assay for CFTR revealed that specifically lowering K18 expression or changing its distribution leads to the delivery of functional deltaF508-CFTR to the plasma membrane. This work suggests a novel function of K18 in CF.
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MESH Headings
- Cell Membrane/metabolism
- Cystic Fibrosis Transmembrane Conductance Regulator/genetics
- Cystic Fibrosis Transmembrane Conductance Regulator/metabolism
- Electrophoresis, Gel, Two-Dimensional
- Electrophoresis, Polyacrylamide Gel
- HeLa Cells
- Humans
- Image Processing, Computer-Assisted
- Immunoblotting
- Immunohistochemistry
- Immunoprecipitation
- Isoelectric Focusing
- Keratin-18
- Keratin-8
- Keratins/metabolism
- Mass Spectrometry/methods
- Microscopy, Fluorescence
- Mutation
- Protein Transport
- Proteomics/methods
- Quinolinium Compounds/pharmacology
- RNA Interference
- RNA, Small Interfering/metabolism
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Temperature
- Time Factors
- Transfection
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Affiliation(s)
- Noélie Davezac
- Inserm U467, Faculté de Médecine Necker Enfants Malades, Paris, France
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17
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Howe KL, Wang A, Hunter MM, Stanton BA, McKay DM. TGFbeta down-regulation of the CFTR: a means to limit epithelial chloride secretion. Exp Cell Res 2004; 298:473-84. [PMID: 15265695 DOI: 10.1016/j.yexcr.2004.04.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2003] [Revised: 04/13/2004] [Indexed: 11/22/2022]
Abstract
Transforming growth factor beta (TGFbeta) is a multifunctional cytokine with effects on many cell types. We recently showed that in addition to epithelial barrier enhancing properties, TGFbeta causes diminished cAMP-driven chloride secretion in colonic epithelia, in a manner that is p38 MAPK-dependent. In this study, we sought to further delineate the mechanism behind TGFbeta diminution of chloride secretion. Using colonic and kidney epithelial cell lines, we found that exposure to TGFbeta causes dramatic changes in the expression and localization of the apical membrane chloride channel, cystic fibrosis transmembrane conductance regulator (CFTR). In TGFbeta-treated colonic epithelia (T84 and HT-29), CFTR mRNA was significantly reduced 2-24 h post-cytokine exposure. At a time consistent with decreased colonic epithelial secretory responses (16 h), TGFbeta treatment caused diminished intracellular CFTR protein expression (confocal microscopy) and reduced channel expression in the apical membrane during stimulated chloride secretion (biotinylation assay). In comparison, polarized kidney epithelia (MDCK) treated with TGFbeta displayed similarly reduced secretory responses to cAMP stimulating agents; however, a perinuclear accumulation of CFTR was observed, contrasting the diffuse cytoplasmic CFTR expression of control cells. Our data indicate that TGFbeta has profound effects on the expression and subcellular localization of an important channel involved in cAMP-driven chloride secretion, and thus suggest TGFbeta represents a key regulator of fluid movement.
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Affiliation(s)
- Kathryn L Howe
- Intestinal Disease Research Programme, Department of Pathology and Molecular Medicine, McMaster University, HSC-3N5C, Hamilton, Ontario, Canada L8N 3Z5
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18
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Liedtke CM, Hubbard M, Wang X. Stability of actin cytoskeleton and PKC-delta binding to actin regulate NKCC1 function in airway epithelial cells. Am J Physiol Cell Physiol 2003; 284:C487-96. [PMID: 12388079 DOI: 10.1152/ajpcell.00357.2002] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Activation of airway epithelial Na-K-2Cl cotransporter (NKCC)1 requires increased activity of protein kinase C (PKC)-delta, which localizes predominantly to the actin cytoskeleton. Prompted by reports of a role for actin in NKCC1 function, we studied a signaling mechanism linking NKCC1 and PKC. Stabilization of actin polymerization with jasplakinolide increased activity of NKCC1, whereas inhibition of actin polymerization with latrunculin B prevented hormonal activation of NKCC1. Protein-protein interactions among NKCC1, actin, and PKC-delta were verified by Western blot analysis of immunoprecipitated proteins. PKC-delta was detected in immunoprecipitates of NKCC1 and vice versa. Actin was also detected in immunoprecipitates of NKCC1 and PKC-delta. Pulldown of endogenous actin revealed the presence of NKCC1 and PKC-delta. Binding of recombinant PKC-delta to NKCC1 was not detected in overlay assays. Rather, activated PKC-delta bound to actin, and this interaction was prevented by a peptide encoding deltaC2, a C2-like domain based on the amino acid sequence of PKC-delta. deltaC2 also blocked stimulation of NKCC1 function by methoxamine. Immunofluorescence and confocal microscopy revealed PKC-delta in the cytosol and cell periphery. Merged images of cells stained for actin and PKC-delta indicated colocalization of PKC-delta and actin at the cell periphery. The results indicate that actin is critical for the activation of NKCC1 through a direct interaction with PKC-delta.
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Affiliation(s)
- Carole M Liedtke
- Warren Alan Bernbaum, M.D. Center for Cystic Fibrosis Research, Department of Pediatrics, Rainbow Babies & Children Hospital, Cleveland, Ohio 44106-4948, USA.
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