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Gerbaldo FE, Sonder E, Fischer V, Frei S, Wang J, Gapp K, Robinson MD, Germain PL. On the identification of differentially-active transcription factors from ATAC-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583825. [PMID: 38496482 PMCID: PMC10942475 DOI: 10.1101/2024.03.06.583825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (a chromVAR-limma workflow with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs - in our case NFkB - at the protein level.
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Affiliation(s)
| | - Emanuel Sonder
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Vincent Fischer
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Selina Frei
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Jiayi Wang
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Katharina Gapp
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Mark D. Robinson
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Pierre-Luc Germain
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
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2
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Uremic toxins activate CREB/ATF1 in endothelial cells related to chronic kidney disease. Biochem Pharmacol 2022; 198:114984. [PMID: 35245485 DOI: 10.1016/j.bcp.2022.114984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/22/2022]
Abstract
Uremic toxins, such as p-cresyl sulfate (PCS) and indoxyl sulfate (IS), contribute to endothelial dysfunction in chronic kidney disease (CKD). This process is mediated by several cellular pathways, but it is unclear whether cAMP-responsive element-binding protein (CREB) and activating transcription factor 1 (ATF1) participate in endothelial dysfunction in uremic conditions despite playing roles in inflammatory modulation. This study aimed to evaluate the expression, activation, and transcriptional activity of CREB/ATF1 in endothelial cells exposed to PCS, IS, and uremic serum (US). In vitro, ATF1 protein levels were increased by PCS and IS, whereas CREB levels were enhanced only by IS. Activation through CREB-Ser133 and ATF1-Ser63 phosphorylation was induced by PCS, IS, and US. We evaluated the CREB/ATF1 transcriptional activity by analyzing the expression of their target genes, including ICAM1, PTGS2, NOX1, and SLC22A6, which are related to endothelial dysfunction through their roles in vascular inflammation, oxidative stress, and cellular uptake of PCS and IS. The expression of ICAM1, PTGS2 and NOX1 genes was increased by PCS, IS, and US, whereas that of SLC22A6 was induced only by IS. KG-501, a CREB inhibitor, restored the inductive effects of PCS on ICAM1, PTGS2, and NOX1 expression; IS on ICAM1, PTGS2 and SLC22A6 expression; and US on NOX1 expression. The presence of CREB and ATF1 was observed in healthy arteries and in arteries of patients with CKD, which were structurally damaged. These findings suggest that CREB/ATF1 is activated by uremic toxins and may play a relevant role in endothelial dysfunction in CKD.
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Nepal N, Arthur S, Butts MR, Singh S, Palaniappan B, Sundaram U. Molecular Mechanism of Stimulation of Na-K-ATPase by Leukotriene D4 in Intestinal Epithelial Cells. Int J Mol Sci 2021; 22:ijms22147569. [PMID: 34299188 PMCID: PMC8303499 DOI: 10.3390/ijms22147569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/03/2022] Open
Abstract
Na-K-ATPase provides a favorable transcellular Na gradient required for the functioning of Na-dependent nutrient transporters in intestinal epithelial cells. The primary metabolite for enterocytes is glutamine, which is absorbed via Na-glutamine co-transporter (SN2; SLC38A5) in intestinal crypt cells. SN2 activity is stimulated during chronic intestinal inflammation, at least in part, secondarily to the stimulation of Na-K-ATPase activity. Leukotriene D4 (LTD4) is known to be elevated in the mucosa during chronic enteritis, but the way in which it may regulate Na-K-ATPase is not known. In an in vitro model of rat intestinal epithelial cells (IEC-18), Na-K-ATPase activity was significantly stimulated by LTD4. As LTD4 mediates its action via Ca-dependent protein kinase C (PKC), Ca levels were measured and were found to be increased. Phorbol 12-myristate 13-acetate (PMA), an activator of PKC, also mediated stimulation of Na-K-ATPase like LTD4, while BAPTA-AM (Ca chelator) and calphostin-C (Cal-C; PKC inhibitor) prevented the stimulation of Na-K-ATPase activity. LTD4 caused a significant increase in mRNA and plasma membrane protein expression of Na-K-ATPase α1 and β1 subunits, which was prevented by calphostin-C. These data demonstrate that LTD4 stimulates Na-K-ATPase in intestinal crypt cells secondarily to the transcriptional increase of Na-K-ATPase α1 and β1 subunits, mediated via the Ca-activated PKC pathway.
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Jespersen N, Barbar E. Emerging Features of Linear Motif-Binding Hub Proteins. Trends Biochem Sci 2020; 45:375-384. [DOI: 10.1016/j.tibs.2020.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
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5
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Vigano S, Alatzoglou D, Irving M, Ménétrier-Caux C, Caux C, Romero P, Coukos G. Targeting Adenosine in Cancer Immunotherapy to Enhance T-Cell Function. Front Immunol 2019; 10:925. [PMID: 31244820 PMCID: PMC6562565 DOI: 10.3389/fimmu.2019.00925] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022] Open
Abstract
T cells play a critical role in cancer control, but a range of potent immunosuppressive mechanisms can be upregulated in the tumor microenvironment (TME) to abrogate their activity. While various immunotherapies (IMTs) aiming at re-invigorating the T-cell-mediated anti-tumor response, such as immune checkpoint blockade (ICB), and the adoptive cell transfer (ACT) of natural or gene-engineered ex vivo expanded tumor-specific T cells, have led to unprecedented clinical responses, only a small proportion of cancer patients benefit from these treatments. Important research efforts are thus underway to identify biomarkers of response, as well as to develop personalized combinatorial approaches that can target other inhibitory mechanisms at play in the TME. In recent years, adenosinergic signaling has emerged as a powerful immuno-metabolic checkpoint in tumors. Like several other barriers in the TME, such as the PD-1/PDL-1 axis, CTLA-4, and indoleamine 2,3-dioxygenase (IDO-1), adenosine plays important physiologic roles, but has been co-opted by tumors to promote their growth and impair immunity. Several agents counteracting the adenosine axis have been developed, and pre-clinical studies have demonstrated important anti-tumor activity, alone and in combination with other IMTs including ICB and ACT. Here we review the regulation of adenosine levels and mechanisms by which it promotes tumor growth and broadly suppresses protective immunity, with extra focus on the attenuation of T cell function. Finally, we present an overview of promising pre-clinical and clinical approaches being explored for blocking the adenosine axis for enhanced control of solid tumors.
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Affiliation(s)
- Selena Vigano
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dimitrios Alatzoglou
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Christine Ménétrier-Caux
- Department of Immunology Virology and Inflammation, INSERM 1052, CNRS 5286, Léon Bérard Cancer Center, Cancer Research Center of Lyon, University of Lyon, University Claude Bernard Lyon 1, Lyon, France
| | - Christophe Caux
- Department of Immunology Virology and Inflammation, INSERM 1052, CNRS 5286, Léon Bérard Cancer Center, Cancer Research Center of Lyon, University of Lyon, University Claude Bernard Lyon 1, Lyon, France
| | - Pedro Romero
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Mechanism of noradrenaline-induced α1-adrenoceptor mediated regulation of Na-K ATPase subunit expression in Neuro-2a cells. Brain Res Bull 2018; 139:157-166. [DOI: 10.1016/j.brainresbull.2018.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 02/08/2018] [Accepted: 02/20/2018] [Indexed: 01/15/2023]
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7
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Huang GL, Liao D, Chen H, Lu Y, Chen L, Li H, Li B, Liu W, Ye C, Li T, Zhu Z, Wang J, Uchida T, Zou Y, Dong Z, He Z. The protein level and transcription activity of activating transcription factor 1 is regulated by prolyl isomerase Pin1 in nasopharyngeal carcinoma progression. Cell Death Dis 2016; 7:e2571. [PMID: 28032861 PMCID: PMC5260992 DOI: 10.1038/cddis.2016.349] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 01/12/2023]
Abstract
The function of activating transcription factor 1 (ATF1) and the mechanism about why ATF1 was over-phosphorylated in nasopharyngeal carcinoma (NPC) progression is completely undiscovered. In this study, a series of experiments both in vitro and in vivo were used to characterize a promotive function of ATF1 in NPC tumorigenesis and identify prolyl isomerase Pin1 as a novel regulator of ATF1 at post-transcription. First, we found that overexpression of ATF1 promoted colony formation in NPC. However, the high protein level of ATF1 in NPC was not resulted from high mRNA level. Then, a direct interaction between Pin1 and ATF1 at Thr184 was demonstrated using mammalian two-hybrid assay and coimmunoprecipitation. Cycloheximide (CHX) treatment indicated Pin1 stabilized the expression of ATF1 at post-transcription level. We confirmed that Pin1 upregulated ATF1 transcriptional activity of Bcl-2 using luciferase reporter assay, quantitative RT-PCR and western blot. Furthermore, the newly identified phosphorylation of ATF1 at Thr184 was suggested to have an important role in ATF1 function of transcription and tumor promotion. Finally, high expression of Pin1 in NPC tissue was found to be positively correlated with ATF1. The ATF1 promoted NPC tumorigenesis was regulated by Pin1 both in vitro and in vivo. All these findings clearly state that Pin1 is a novel regulator of ATF1 at Thr184 and thereby enhances ATF1 transcription activity and tumorigenesis promotive function in NPC.
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Affiliation(s)
- Guo-Liang Huang
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Dan Liao
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China.,Department of Gynaecology and Obstetrics, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, China
| | - Hua Chen
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Yan Lu
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China.,Research Institute of Clinical Medicine, The First People's Hospital of Shunde Affiliate to Southern Medical University, Foshan, China
| | - Liyong Chen
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Huahui Li
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Binbin Li
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Weilong Liu
- Experimental Animal Center, Shenzhen Third People's Hospital, Shenzhen, China
| | - Caiguo Ye
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Tong Li
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Zhu Zhu
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Jian Wang
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Takafumi Uchida
- Department of Molecular Cell Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, Japan
| | - Ying Zou
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Zhiwei He
- China-American Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Key Laboratory for Epigenetics of Dongguan City, Key Laboratory for Medical Molecular Diagnostics of Guangdong Province, Dongguan, China
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Varicella-Zoster Virus Activates CREB, and Inhibition of the pCREB-p300/CBP Interaction Inhibits Viral Replication In Vitro and Skin Pathogenesis In Vivo. J Virol 2016; 90:8686-97. [PMID: 27440893 PMCID: PMC5021407 DOI: 10.1128/jvi.00920-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Varicella-zoster virus (VZV) is an alphaherpesvirus that causes varicella upon primary infection and zoster upon reactivation from latency in sensory ganglion neurons. The replication of herpesviruses requires manipulation of cell signaling pathways. Notably, CREB, a factor involved in the regulation of several cellular processes, is activated upon infection of T cells with VZV. Here, we report that VZV infection also induced CREB phosphorylation in fibroblasts and that XX-650-23, a newly identified inhibitor of the phosphorylated-CREB (pCREB) interaction with p300/CBP, restricted cell-cell spread of VZV in vitro CREB phosphorylation did not require the viral open reading frame 47 (ORF47) and ORF66 kinases encoded by VZV. Evaluating the biological relevance of these observations during VZV infection of human skin xenografts in the SCID mouse model of VZV pathogenesis showed both that pCREB was upregulated in infected skin and that treatment with XX-650-23 reduced infectious-virus production and limited lesion formation compared to treatment with a vehicle control. Thus, processes of CREB activation and p300/CBP binding are important for VZV skin infection and may be targeted for antiviral drug development. IMPORTANCE Varicella-zoster virus (VZV) is a common pathogen that causes chicken pox and shingles. As with all herpesviruses, the infection is acquired for life, and the virus can periodically reactivate from latency. Although VZV infection is usually benign with few or no deleterious consequences, infection can be life threatening in immunocompromised patients. Otherwise healthy elderly individuals who develop zoster as a consequence of viral reactivation are at risk for postherpetic neuralgia (PHN), a painful and long-lasting complication. Current vaccines use a live attenuated virus that is usually safe but cannot be given to many immunodeficient patients and retains the capacity to establish latency and reactivate, causing zoster. Antiviral drugs are effective against severe VZV infections but have little impact on PHN. A better understanding of virus-host cell interactions is relevant for developing improved therapies to safely interfere with cellular processes that are crucial for VZV pathogenesis.
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Yang X, Hao H, Xia Z, Xu G, Cao Z, Chen X, Liu S, Zhu Y. Soluble IL-6 Receptor and IL-27 Subunit p28 Protein Complex Mediate the Antiviral Response through the Type III IFN Pathway. THE JOURNAL OF IMMUNOLOGY 2016; 197:2369-81. [PMID: 27527594 DOI: 10.4049/jimmunol.1600627] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/13/2016] [Indexed: 02/07/2023]
Abstract
Previously, we demonstrated that the soluble IL-6R (sIL-6R) plays an important role in the host antiviral response through induction of type I IFN and sIL-6R-mediated antiviral action via the IL-27 subunit p28; however, the mechanism that underlies sIL-6R and p28 antiviral action and whether type III IFN is involved remain unknown. In this study, we constructed a sIL-6R and p28 fusion protein (sIL-6R/p28 FP) and demonstrated that the fusion protein has stronger antiviral activity than sIL-6R alone. Consequently, knockout of sIL-6R inhibited virus-triggered IFN-λ1 expression. In addition, sIL-6R/p28 FP associated with mitochondrial antiviral signaling protein and TNFR-associated factor 6, the retinoic acid-inducible gene I adapter complex, and the antiviral activity mediated by sIL-6R/p28 FP was dependent on mitochondrial antiviral signaling protein. Furthermore, significantly reduced binding of p50/p65 and IFN regulatory factor 3 to the IFN-λ1 promoter was observed in sIL-6R knockout cells compared with the control cells. Interestingly, a novel heterodimer of c-Fos and activating transcription factor 1 was identified as a crucial transcriptional activator of IFN-λ1 The sIL-6R/p28 FP upregulated IFN-λ1 expression by increasing the binding abilities of c-Fos and activating transcription factor 1 to the IFN-λ1 promoter via the p38 MAPK signaling pathway. In conclusion, these results demonstrate the important role of sIL-6R/p28 FP in mediating virus-induced type III IFN production.
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Affiliation(s)
- Xiaodan Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hua Hao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhangchuan Xia
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Gang Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongying Cao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xueyuan Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shi Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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10
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Li Z, Langhans SA. Transcriptional regulators of Na,K-ATPase subunits. Front Cell Dev Biol 2015; 3:66. [PMID: 26579519 PMCID: PMC4620432 DOI: 10.3389/fcell.2015.00066] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
The Na,K-ATPase classically serves as an ion pump creating an electrochemical gradient across the plasma membrane that is essential for transepithelial transport, nutrient uptake and membrane potential. In addition, Na,K-ATPase also functions as a receptor, a signal transducer and a cell adhesion molecule. With such diverse roles, it is understandable that the Na,K-ATPase subunits, the catalytic α-subunit, the β-subunit and the FXYD proteins, are controlled extensively during development and to accommodate physiological needs. The spatial and temporal expression of Na,K-ATPase is partially regulated at the transcriptional level. Numerous transcription factors, hormones, growth factors, lipids, and extracellular stimuli modulate the transcription of the Na,K-ATPase subunits. Moreover, epigenetic mechanisms also contribute to the regulation of Na,K-ATPase expression. With the ever growing knowledge about diseases associated with the malfunction of Na,K-ATPase, this review aims at summarizing the best-characterized transcription regulators that modulate Na,K-ATPase subunit levels. As abnormal expression of Na,K-ATPase subunits has been observed in many carcinoma, we will also discuss transcription factors that are associated with epithelial-mesenchymal transition, a crucial step in the progression of many tumors to malignant disease.
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Affiliation(s)
- Zhiqin Li
- Nemours Center for Childhood Cancer Research, Nemours/Alfred I. duPont Hospital for Children Wilmington, DE, USA
| | - Sigrid A Langhans
- Nemours Center for Childhood Cancer Research, Nemours/Alfred I. duPont Hospital for Children Wilmington, DE, USA
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11
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Roosterman D. Agonist-dependent and -independent dopamine-1-like receptor signalling differentially regulates downstream effectors. FEBS J 2014; 281:4792-804. [PMID: 25154512 DOI: 10.1111/febs.13018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 07/25/2014] [Accepted: 08/21/2014] [Indexed: 12/17/2022]
Abstract
De-regulation of energy metabolism by the dopaminergic system is linked to neurological diseases such as schizophrenia and bipolar disorder. Inverse agonists are thought to be more beneficial in treating neurological diseases than neutral antagonists, but only limited experimental data are available regarding the impact of constitutive signalling on energy metabolism. The aim of the present study was to assess the impact of constitutive dopamine-1 receptor (D1R) and dopamine-5 receptor (D5R) signalling on downstream targets in transiently and stably transfected HEK293T cells. The high constitutive activity of D5R was accompanied by increased Na(+)/H(+) exchanger (NHE) activity and accelerated glucose degradation due to increased transcription and translation of the Na, K-ATPase-α3 and NHE-2. Chronic treatment with an agonist increased the mRNA levels of the α2 Na,K-ATPase, NHE-2 and NHE-3. Constitutive D5R activation of a cAMP response element-based reporter was regulated by G protein-coupled receptor kinase 2, but this did not affect the cell-surface abundance of the receptor. Our data suggest that constitutive and agonist-induced activity of D5R differentially regulates the activity and expression of proteins.
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12
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Giansanti P, Stokes MP, Silva JC, Scholten A, Heck AJR. Interrogating cAMP-dependent kinase signaling in Jurkat T cells via a protein kinase A targeted immune-precipitation phosphoproteomics approach. Mol Cell Proteomics 2013; 12:3350-9. [PMID: 23882029 DOI: 10.1074/mcp.o113.028456] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the past decade, mass-spectrometry-based methods have emerged for the quantitative profiling of dynamic changes in protein phosphorylation, allowing the behavior of thousands of phosphorylation sites to be monitored in a single experiment. However, when one is interested in specific signaling pathways, such shotgun methodologies are not ideal because they lack selectivity and are not cost and time efficient with respect to instrument and data analysis time. Here we evaluate and explore a peptide-centric antibody generated to selectively enrich peptides containing the cAMP-dependent protein kinase (PKA) consensus motif. This targeted phosphoproteomic strategy is used to profile temporal quantitative changes of potential PKA substrates in Jurkat T lymphocytes upon prostaglandin E2 (PGE2) stimulation, which increases intracellular cAMP, activating PKA. Our method combines ultra-high-specificity motif-based immunoaffinity purification with cost-efficient stable isotope dimethyl labeling. We identified 655 phosphopeptides, of which 642 (i.e. 98%) contained the consensus motif [R/K][R/K/X]X[pS/pT]. When our data were compared with a large-scale Jurkat T-lymphocyte phosphoproteomics dataset containing more than 10,500 phosphosites, a minimal overlap of 0.2% was observed. This stresses the need for such targeted analyses when the interest is in a particular kinase. Our data provide a resource of likely substrates of PKA, and potentially some substrates of closely related kinases. Network analysis revealed that about half of the observed substrates have been implicated in cAMP-induced signaling. Still, the other half of the here-identified substrates have been less well characterized, representing a valuable resource for future research.
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Affiliation(s)
- Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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13
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Dietze R, Konrad L, Shihan M, Kirch U, Scheiner-Bobis G. Cardiac glycoside ouabain induces activation of ATF-1 and StAR expression by interacting with the α4 isoform of the sodium pump in Sertoli cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:511-9. [DOI: 10.1016/j.bbamcr.2012.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 11/20/2012] [Accepted: 11/26/2012] [Indexed: 01/27/2023]
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14
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Transcriptional activity of neural retina leucine zipper (Nrl) is regulated by c-Jun N-terminal kinase and Tip60 during retina development. Mol Cell Biol 2012; 32:1720-32. [PMID: 22354990 DOI: 10.1128/mcb.06440-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Neural retina leucine zipper (Nrl), a key basic motif leucine zipper (bZIP) transcription factor, modulates rod photoreceptor differentiation by activating rod-specific target genes. In searching for factors that might couple with Nrl to modulate its transcriptional activity through posttranslational modification, we observed the novel interactions of Nrl with c-Jun N-terminal kinase 1 (JNK1) and HIV Tat-interacting protein 60 (Tip60). JNK1 directly interacted with and phosphorylated Nrl at serine 50, which enhanced Nrl transcriptional activity on the rhodopsin and Ppp2r5c promoters. Use of an inactive JNK1 mutant or treatment with a JNK inhibitor (SP600125) significantly reduced JNK1-mediated phosphorylation and transcriptional activity of Nrl in cultured retinal explants. We also found that Nrl activated rhodopsin and Ppp2r5c transcription by recruiting Tip60 to promote histone H3/H4 acetylation. The binding affinity of phospho-Nrl for Tip60 was significantly greater than that of the unphosphorylated Nrl. Thus, the histone acetyltransferase-containing Tip60 behaved as a coactivator in the Nrl-dependent transcriptional regulation of the rhodopsin and Ppp2r5c genes in the developing mouse retina. A transcriptional network of interactive proteins, including Nrl, JNK1, and Tip60, may be required to precisely control spatiotemporal photoreceptor-specific gene expression during retinal development.
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Fajas L, Paul C, Vié A, Estrach S, Medema R, Blanchard JM, Sardet C, Vignais ML. Cyclin A is a mediator of p120E4F-dependent cell cycle arrest in G1. Mol Cell Biol 2001; 21:2956-66. [PMID: 11283272 PMCID: PMC86923 DOI: 10.1128/mcb.21.8.2956-2966.2001] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
E4F is a ubiquitously expressed GLI-Krüppel-related transcription factor which has been identified for its capacity to regulate transcription of the adenovirus E4 gene in response to E1A. However, cellular genes regulated by E4F are still unknown. Some of these genes are likely to be involved in cell cycle progression since ectopic p120E4F expression induces cell cycle arrest in G1. Although p21WAF1 stabilization was proposed to mediate E4F-dependent cell cycle arrest, we found that p120E4F can induce a G1 block in p21(-/-) cells, suggesting that other proteins are essential for the p120E4F-dependent block in G1. We show here that cyclin A promoter activity can be repressed by p120E4F and that this repression correlates with p120E4F binding to the cyclic AMP-responsive element site of the cyclin A promoter. In addition, enforced expression of cyclin A releases p120E4F-arrested cells from the G1 block. These data identify the cyclin A gene as a cellular target for p120E4F and suggest a mechanism for p120E4F-dependent cell cycle regulation.
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Affiliation(s)
- L Fajas
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535, IFR 24, 34293 Montpellier Cedex 5, France
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Zhou J, Finch PW. Identification of a novel transcriptional regulatory element within the promoter region of the keratinocyte growth factor gene that mediates inducibility to cyclic AMP. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1446:71-81. [PMID: 10395920 DOI: 10.1016/s0167-4781(99)00069-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Keratinocyte growth factor (KGF) plays a critical role for the normal development and morphogenesis of many different tissues and organs. Furthermore, its expression is induced during wound healing and in various chronic inflammatory diseases. To determine the molecular mechanisms which regulate KGF gene induction at the transcriptional level, we carried out in vitro studies using the human KGF promoter. We have identified a novel regulatory element, TGAGGTCAG, located between -39 and -46 bp (relative to the transcription start site) in the KGF basal promoter region, which binds to inducible transcription factors as determined by electrophoretic mobility shift assay. When cloned in front of a heterologous SV40 promoter this region conferred inducibility to forskolin, a stimulator of adenylate cyclase. In contrast, various mutated forms of this region were either partially or completely impaired in their ability to mediate induction to forskolin. The TGAGGTCAG sequence shared homology to both the cAMP responsive element (CRE) and CCAAT/enhancer binding protein (C/EBP) consensus binding sites. An oligonucleotide comprising a consensus CRE binding site partially competed for the nuclear protein binding to the TGAGGTCAG site. Gel mobility supershift assays indicated that two members of the activating transcription factor (ATF) family of CRE binding proteins, ATF1 and ATF2, were part of the nuclear protein complex bound to this regulatory region. Furthermore, purified recombinant ATF2 was able to directly recognize and bind the TGAGGTCAG sequence. In contrast, no evidence was obtained for C/EBP transcription factors being part of the complex. These results suggest that members of the ATF family are involved in mediating the transcriptional regulation of the KGF gene in response to extracellular stimuli via a novel CRE regulatory element.
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Affiliation(s)
- J Zhou
- The Derald H. Ruttenberg Cancer Center, Box 1130, Mount Sinai School of Medicine, 1 Gustave L. Levy Place, New York, NY 10029-6574, USA
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Kon N, Schroeder SC, Krawchuk MD, Wahls WP. Regulation of the Mts1-Mts2-dependent ade6-M26 meiotic recombination hot spot and developmental decisions by the Spc1 mitogen-activated protein kinase of fission yeast. Mol Cell Biol 1998; 18:7575-83. [PMID: 9819443 PMCID: PMC109338 DOI: 10.1128/mcb.18.12.7575] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/1998] [Accepted: 09/03/1998] [Indexed: 11/20/2022] Open
Abstract
The M26 meiotic recombination hot spot in the ade6 gene of Schizosaccharomyces pombe is activated by the heterodimeric M26 binding protein Mts1-Mts2. The individual Mts1 (Atf1, Gad7) and Mts2 (Pcr1) proteins are also transcription factors involved in developmental decisions. We report that the Mts proteins are key effectors of at least two distinct classes of developmental decisions regulated by the mitogen-activated protein (MAP) kinase cascade. The first class (osmoregulation, spore viability, and spore quiescence) requires the Spc1 MAP kinase and the Mts1 protein but does not require the Mts2 protein. The second class (mating, meiosis, and recombination hot spot activation) requires the Spc1 kinase and the Mts1-Mts2 heterodimer. Northern and Western blotting eliminated any significant role for the Spc1 kinase in regulating the expression levels of the Mts proteins. Gel mobility shift experiments indicated that the Mts1-Mts2 heterodimer does not need to be phosphorylated to bind to ade6-M26 DNA in vitro. However, in vivo dimethyl sulfate footprinting demonstrated that protein-DNA interaction within cells is dependent upon the Spc1 MAP kinase, which phosphorylates the Mts1 protein. Thus, the Spc1 kinase helps regulate the effector activities of the Mts1-Mts2 heterodimer in part by modulating its ability to occupy the M26 DNA site in vivo. Meiotic recombination hot spot function is likely the result of DNA conformational changes imparted by binding of the Mts1-Mts2 meiotic transcription factor.
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Affiliation(s)
- N Kon
- Departments of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Abstract
Cyclic adenosine monophosphate (cAMP) is a ubiquitous second messenger produced in cells in response to hormones and nutrients. The production of cAMP is dependent upon the actions of many different proteins that affect its synthesis and degradation. An important function of cAMP is to activate the phosphorylating enzyme, protein kinase A. The key roles of cAMP and protein kinase A in the phosphorylation and regulation of enzyme substrates involved in intermediary metabolism are well known. A newly discovered role for protein kinase A is in the phosphorylation and activation of transcription factors that are critical for the control of the transcription of genes in response to elevated levels of cAMP.
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Affiliation(s)
- P B Daniel
- Laboratory of Molecular Endocrinology, Massachusetts General Hospital, Boston 02114, USA
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Abstract
Transcription activation via activating transcription factor cyclic AMP response element binding (ATF/CREB) sites in vitro was explored using transcription and permanganate assay for open complex formation. These sites were used to drive transcription from an adenovirus major late core sequence. Under conditions where activation is strong, 20-50-fold, ATF/CREB is required for preinitiation complexes to reach the open complex stage. Complete opening requires activator, ATP, and initiating nucleotides. In exploration of postinitiation steps, no stimulation of promoter clearance was observed but a modest stimulation of the rate of continuous transcription occurred. High amounts of DNA template, commonly used in in vitro studies, allows some templates to open without activator, but leaves the nucleotide requirements intact. This leads to a drastic lowering of the dependence on ATF/CREB. Taken together, the data indicate that ATF/CREB activates this system primarily by stimulating the formation of functional preinitiation complexes.
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Affiliation(s)
- B S Wolner
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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Kobayashi M, Kawakami K. Synergism of the ATF/CRE site and GC box in the housekeeping Na,K-ATPase alpha1 subunit gene is essential for constitutive expression. Biochem Biophys Res Commun 1997; 241:169-74. [PMID: 9405252 DOI: 10.1006/bbrc.1997.7781] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Na,K-ATPase alpha1 subunit gene is constitutively expressed in a wide variety of tissues. Our previous studies revealed that the promoter region between -77 and +17 of the transcription initiation site of the rat Na,K-ATPase alpha1 subunit gene (Atp1a1) is sufficient for the promoter activity. In this region, an ATF/CRE site with an adjacent GC box exists. To elucidate how these sites are involved in the promoter activity, we analyzed effects of point mutations at these sites on transcription by in vitro transcription assays using nuclear extracts prepared from various rat tissues. Mutation at either site resulted in dramatic reduction of the promoter activity in all nuclear extracts, while mutation at both sites did not lead to further reduction. These results indicate that the ATF/CRE site and GC box are both essential for promoter activity and show synergistic activation. Electrophoretic mobility shift assay indicated that Sp1 and/or Sp3 bind to the GC box, and ATF1-CREB heterodimer binds to the ATF/CRE site. Since an element, ATF/CRE site-GC box, is conserved in mammalian Na,K-ATPase alpha1 subunit genes and in other constitutive promoters, we propose that this element is a critical unit for constitutive expression.
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Affiliation(s)
- M Kobayashi
- Department of Biology, Jichi Medical School, Minamikawachi, Tochigi, Kawachi, 329-0498, Japan
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