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Zhao Y, Xing C, Deng Y, Ye C, Peng H. HIF-1α signaling: Essential roles in tumorigenesis and implications in targeted therapies. Genes Dis 2024; 11:234-251. [PMID: 37588219 PMCID: PMC10425810 DOI: 10.1016/j.gendis.2023.02.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/24/2022] [Accepted: 02/12/2023] [Indexed: 08/18/2023] Open
Abstract
The hypoxic microenvironment is an essential characteristic of most malignant tumors. Notably, hypoxia-inducible factor-1 alpha (HIF-1α) is a key regulatory factor of cellular adaptation to hypoxia, and many critical pathways are correlated with the biological activity of organisms via HIF-1α. In the intra-tumoral hypoxic environment, HIF-1α is highly expressed and contributes to the malignant progression of tumors, which in turn results in a poor prognosis in patients. Recently, it has been indicated that HIF-1α involves in various critical processes of life events and tumor development via regulating the expression of HIF-1α target genes, such as cell proliferation and apoptosis, angiogenesis, glucose metabolism, immune response, therapeutic resistance, etc. Apart from solid tumors, accumulating evidence has revealed that HIF-1α is also closely associated with the development and progression of hematological malignancies, such as leukemia, lymphoma, and multiple myeloma. Targeted inhibition of HIF-1α can facilitate an increased sensitivity of patients with malignancies to relevant therapeutic agents. In the review, we elaborated on the basic structure and biological functions of HIF-1α and summarized their current role in various malignancies. It is expected that they will have future potential for targeted therapy.
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Affiliation(s)
- Yan Zhao
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Cheng Xing
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yating Deng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Can Ye
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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2
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Golijanin B, Malshy K, Khaleel S, Lagos G, Amin A, Cheng L, Golijanin D, Mega A. Evolution of the HIF targeted therapy in clear cell renal cell carcinoma. Cancer Treat Rev 2023; 121:102645. [PMID: 37879247 DOI: 10.1016/j.ctrv.2023.102645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/11/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer, affecting hundreds of thousands of people worldwide and can affect people of any age. The pathogenesis of ccRCC is most commonly due to biallelic loss of the tumor suppressor gene VHL. VHL is the recognition subunit of an E3-ubiquitin-ligase-complex essential for degradation of the hypoxia-inducible factors (HIF) 1α and 2α. Dysfunctional degradation of HIF results in overaccumulation, which is particularly concerning with the HIF2α subunit. This leads to nuclear translocation, dimerization, and transactivation of numerous HIF-regulated genes responsible for cell survival and proliferation in ccRCC. FDA-approved therapies for RCC have primarily focused on targeting downstream effectors of HIF, then incorporated immunotherapeutics, and now, novel approaches are moving back to HIF with a focus on interfering with upstream targets. This review summarizes the role of HIF in the pathogenesis of ccRCC, novel HIF2α-focused therapeutic approaches, and opportunities for ccRCC treatment.
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Affiliation(s)
- Borivoj Golijanin
- The Minimally Invasive Urology Institute at The Miriam Hospital, Division of Urology, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States.
| | - Kamil Malshy
- The Minimally Invasive Urology Institute at The Miriam Hospital, Division of Urology, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States
| | - Sari Khaleel
- The Minimally Invasive Urology Institute at The Miriam Hospital, Division of Urology, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States
| | - Galina Lagos
- Lifespan Cancer Institute, Department of Hematology and Oncology, The Miriam Hospital, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States
| | - Ali Amin
- Department of Pathology and Laboratory Medicine, The Miriam Hospital, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, The Miriam Hospital, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States
| | - Dragan Golijanin
- The Minimally Invasive Urology Institute at The Miriam Hospital, Division of Urology, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States
| | - Anthony Mega
- Lifespan Cancer Institute, Department of Hematology and Oncology, The Miriam Hospital, Lifespan Academic Medical Center, The Legorreta Cancer Center at Brown University, Warren Alpert Medical School of Brown University, Providence, RI 02906, United States
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3
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Pinto CJG, Ávila-Gálvez MÁ, Lian Y, Moura-Alves P, Nunes Dos Santos C. Targeting the aryl hydrocarbon receptor by gut phenolic metabolites: A strategy towards gut inflammation. Redox Biol 2023; 61:102622. [PMID: 36812782 PMCID: PMC9958510 DOI: 10.1016/j.redox.2023.102622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
The Aryl Hydrocarbon Receptor (AHR) is a ligand-dependent transcription factor able to control complex transcriptional processes in several cell types, which has been correlated with various diseases, including inflammatory bowel diseases (IBD). Numerous studies have described different compounds as ligands of this receptor, like xenobiotics, natural compounds, and several host-derived metabolites. Dietary (poly)phenols have been studied regarding their pleiotropic activities (e.g., neuroprotective and anti-inflammatory), but their AHR modulatory capabilities have also been considered. However, dietary (poly)phenols are submitted to extensive metabolism in the gut (e.g., gut microbiota). Thus, the resulting gut phenolic metabolites could be key players modulating AHR since they are the ones that reach the cells and may exert effects on the AHR throughout the gut and other organs. This review aims at a comprehensive search for the most abundant gut phenolic metabolites detected and quantified in humans to understand how many have been described as AHR modulators and what could be their impact on inflammatory gut processes. Even though several phenolic compounds have been studied regarding their anti-inflammatory capacities, only 1 gut phenolic metabolite, described as AHR modulator, has been evaluated on intestinal inflammatory models. Searching for AHR ligands could be a novel strategy against IBD.
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Affiliation(s)
- Catarina J G Pinto
- iNOVA4Health, NOVA Medical School
- Faculdade de Ciências Médicas, NMS
- FCM, Universidade Nova de Lisboa, Lisboa, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - María Ángeles Ávila-Gálvez
- iNOVA4Health, NOVA Medical School
- Faculdade de Ciências Médicas, NMS
- FCM, Universidade Nova de Lisboa, Lisboa, Portugal; iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, Portugal
| | - Yilong Lian
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, Oxford, United Kingdom
| | - Pedro Moura-Alves
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, Oxford, United Kingdom.
| | - Cláudia Nunes Dos Santos
- iNOVA4Health, NOVA Medical School
- Faculdade de Ciências Médicas, NMS
- FCM, Universidade Nova de Lisboa, Lisboa, Portugal; iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, Portugal.
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4
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Pajarillo E, Nyarko-Danquah I, Digman A, Multani HK, Kim S, Gaspard P, Aschner M, Lee E. Mechanisms of manganese-induced neurotoxicity and the pursuit of neurotherapeutic strategies. Front Pharmacol 2022; 13:1011947. [PMID: 36605395 PMCID: PMC9808094 DOI: 10.3389/fphar.2022.1011947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/01/2022] [Indexed: 01/07/2023] Open
Abstract
Chronic exposure to elevated levels of manganese via occupational or environmental settings causes a neurological disorder known as manganism, resembling the symptoms of Parkinson's disease, such as motor deficits and cognitive impairment. Numerous studies have been conducted to characterize manganese's neurotoxicity mechanisms in search of effective therapeutics, including natural and synthetic compounds to treat manganese toxicity. Several potential molecular targets of manganese toxicity at the epigenetic and transcriptional levels have been identified recently, which may contribute to develop more precise and effective gene therapies. This review updates findings on manganese-induced neurotoxicity mechanisms on intracellular insults such as oxidative stress, inflammation, excitotoxicity, and mitophagy, as well as transcriptional dysregulations involving Yin Yang 1, RE1-silencing transcription factor, transcription factor EB, and nuclear factor erythroid 2-related factor 2 that could be targets of manganese neurotoxicity therapies. This review also features intracellular proteins such as PTEN-inducible kinase 1, parkin, sirtuins, leucine-rich repeat kinase 2, and α-synuclein, which are associated with manganese-induced dysregulation of autophagy/mitophagy. In addition, newer therapeutic approaches to treat manganese's neurotoxicity including natural and synthetic compounds modulating excitotoxicity, autophagy, and mitophagy, were reviewed. Taken together, in-depth mechanistic knowledge accompanied by advances in gene and drug delivery strategies will make significant progress in the development of reliable therapeutic interventions against manganese-induced neurotoxicity.
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Affiliation(s)
- Edward Pajarillo
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Ivan Nyarko-Danquah
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Alexis Digman
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Harpreet Kaur Multani
- Department of Biology, College of Science and Technology, Florida A&M University, Tallahassee, FL, United States
| | - Sanghoon Kim
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Patric Gaspard
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY, United States
| | - Eunsook Lee
- Department of Pharmaceutical Science, College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, United States
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5
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Wang Y, He H, Chen J, Song Z, Pan X, Lan T, Wang G. Effects of glycolysis and polyamine predation on intestinal epithelial barrier in colorectal cancer. Front Oncol 2022; 12:961257. [PMID: 35912204 PMCID: PMC9337861 DOI: 10.3389/fonc.2022.961257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/24/2022] [Indexed: 01/15/2023] Open
Abstract
Colorectal cancer (CRC) is the second most lethal cancer and the third most common cancer in the world, and its prognosis is severely affected by high intestinal mucosal permeability and increasing tumor burden. Studies have shown that the expression of hypoxia induce factor 1α (HIF1α) is up-regulated in a variety of tumor tissues, which is related to multiple metabolic reprogramming of tumor cells. However, the role of HIF1α in CRC tumor growth, tumor polyamine metabolism and intestinal mucosal barrier damage has not been studied. Here, we constructed different types of CRC tumor-bearing mice models by inoculating HCT116 cells with different levels of HIF1α expression (knockdown, wild type, overexpression) in the armpits of mice to explore the upstream and downstream regulators of HIF1α, the effects of HIF1α on the growth of CRC, and the CRC polyamine metabolism and its effect on the intestinal mucosal barrier. We found that with the increase of HIF1 gene expression, tumor growth was promoted and intestinal mucosal permeability was increased. The expression of glycolysis-related proteins was up-regulated, the rate-limiting enzyme ODC of polyamine synthesis was decreased, and the transfer protein of polyamine was increased. HPLC showed that the polyamine content in the tumor tissue of the overexpression group HIF1α OE was higher than that of the wild group HIF1α (+/+), and higher than that of the knockdown group HIF1α (-/-), but the content of polyamines in intestinal mucosa was the opposite. After supplementation of exogenous polyamines, the content of polyamines in intestinal mucosa and tumor tissue increased, and the damage of intestinal mucosa was alleviated. In conclusion, upon activation of the MYC/HIF1 pathway, tumor glycolysis is enhanced, tumors require more energy and endogenous polyamine synthesis is reduced. Therefore, in order to meet its growth needs, tumor will rob polyamines in the intestinal mucosa, resulting in intestinal mucosal epithelial barrier dysfunction.
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Affiliation(s)
| | | | | | | | | | - Tian Lan
- *Correspondence: Tian Lan, ; Guixiang Wang,
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6
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Tu C, Huang G, Li C, Cheng L, Min Y, Li H, Mao D, Xiong F. Exploring Mechanisms by Which Danggui Buxue Decoction Regulates Inflammation and Improves Renal Anemia Based on Network Pharmacology. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221093905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Renal anemia occurs frequently in patients with chronic kidney disease (CKD) and is related to chronic inflammation. Danggui Buxue Decoction (DBD) can treat anemia and improve the chronic inflammation. However, whether DBD treatment attenuates anemia by regulating inflammation in CKD patients with renal anemia is unknown. Therefore, this study explored inflammation-related network targets of DBD in renal anemia therapy and verified the interaction between DBD active ingredients and inflammatory proteins by molecular docking. Methods: The main effective components and targets of DBD were screened using the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. Renal anemia-related biomolecules were searched in the GeneCards, OMIM, TTD, Pharmgkb, and DrugBank databases. Protein-protein interaction (PPI) data were downloaded from the STRING database and core targets were obtained. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for core targets were performed. Finally, active ingredients and core biomolecules were determined using molecular docking. Results: Twenty-two active components and 158 targets for DBD treatment of renal anemia were screened, and an “ingredient-target” network was constructed. Twenty core target genes were screened from the PPI data. Vascular endothelial growth factor A, Signal Transducer and Activator of transcription 1, C-X-C motif chemokine ligand 8, post-transcriptional gene silencing 2, and interleukin (IL)-1β were identified as inflammatory proteins. GO items related to inflammation and DBD included lipopolysaccharide, cellular response to chemical stress, and oxidative stress-related reactions. KEGG enrichment analyses showed that core inflammatory pathways mainly involved the IL-17 signaling pathway, tumor necrosis factor signaling pathway, and phosphoinositide 3-kinase-protein kinase B signaling pathway. Molecular docking results indicated that the binding energy of quercetin, an active ingredient of DBD, to the 5 core proteins was less than −6 kcal·mol−1. Conclusion: DBD might have protective effects against renal anemia by improving inflammation. Quercetin might modulate multiple inflammatory proteins and pathways.
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Affiliation(s)
- Can Tu
- Department of Nephrology, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guirui Huang
- Department of Respiratory, The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Chuang Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Li Cheng
- Department of Nephrology, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
| | - Yonglong Min
- Department of Nephrology, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
| | - Hongbo Li
- Department of Nephrology, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
| | - Dongdong Mao
- Department of Nephrology, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
| | - Fei Xiong
- Department of Nephrology, Wuhan Hospital of Traditional Chinese and Western Medicine, Wuhan, China
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7
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Wang X, Du ZW, Xu TM, Wang XJ, Li W, Gao JL, Li J, Zhu H. HIF-1α Is a Rational Target for Future Ovarian Cancer Therapies. Front Oncol 2022; 11:785111. [PMID: 35004308 PMCID: PMC8739787 DOI: 10.3389/fonc.2021.785111] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/06/2021] [Indexed: 01/17/2023] Open
Abstract
Ovarian cancer is the eighth most commonly diagnosed cancer among women worldwide. Even with the development of novel drugs, nearly one-half of the patients with ovarian cancer die within five years of diagnosis. These situations indicate the need for novel therapeutic agents for ovarian cancer. Increasing evidence has shown that hypoxia-inducible factor-1α(HIF-1α) plays an important role in promoting malignant cell chemoresistance, tumour metastasis, angiogenesis, immunosuppression and intercellular interactions. The unique microenvironment, crosstalk and/or interaction between cells and other characteristics of ovarian cancer can influence therapeutic efficiency or promote the disease progression. Inhibition of the expression or activity of HIF-1α can directly or indirectly enhance the therapeutic responsiveness of tumour cells. Therefore, it is reasonable to consider HIF-1α as a potential therapeutic target for ovarian cancer. In this paper, we summarize the latest research on the role of HIF-1α and molecules which can inhibit HIF-1α expression directly or indirectly in ovarian cancer, and drug clinical trials about the HIF-1α inhibitors in ovarian cancer or other solid malignant tumours.
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Affiliation(s)
- Xin Wang
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - Zhen-Wu Du
- Department of Orthopaedics, The Second Hospital of Jilin University, Changchun, China.,Research Center, The Second Hospital of Jilin University, Changchun, China
| | - Tian-Min Xu
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - Xiao-Jun Wang
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - Wei Li
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - Jia-Li Gao
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - Jing Li
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
| | - He Zhu
- Department of Obstetrics and Gynaecology, The Second Hospital of Jilin University, Changchun, China
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8
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Nyamsuren G, Rapp G, Dihazi H, Zeisberg EM, Tampe D, Tampe B, Zeisberg M. PP2A phosphatase inhibition is anti-fibrotic through Ser77 phosphorylation-mediated ARNT/ARNT homodimer formation. Sci Rep 2021; 11:24075. [PMID: 34912030 PMCID: PMC8674365 DOI: 10.1038/s41598-021-03523-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 11/02/2021] [Indexed: 11/09/2022] Open
Abstract
Aryl hydrocarbon receptor nuclear translocator (ARNT) mediates anti-fibrotic activity in kidney and liver through induction of ALK3-receptor expression and subsequently increased Smad1/5/8 signaling. While expression of ARNT can be pharmacologically induced by sub-immunosuppressive doses of FK506 or by GPI1046, its anti-fibrotic activity is only realized when ARNT-ARNT homodimers form, as opposed to formation of ARNT-AHR or ARNT-HIF1α heterodimers. Mechanisms underlying ARNTs dimerization decision to specifically form ARNT–ARNT homodimers and possible cues to specifically induce ARNT homodimerization have been previously unknown. Here, we demonstrate that phosphorylation of the Ser77 residue is critical for ARNT–ARNT homodimer formation and stabilization. We further demonstrate that inhibition of PP2A phosphatase activity by LB100 enhances ARNT–ARNT homodimers both in vivo and in vitro (mouse tubular epithelial cells and human embryonic kidney cells). In murine models of kidney fibrosis, and also of liver fibrosis, combinations of FK506 or GPI1046 (to induce ARNT expression) with LB100 (to enhance ARNT homodimerization) elicit additive anti-fibrotic activities. Our study provides additional evidence for the anti-fibrotic activity of ARNT–ARNT homodimers and reveals Ser77 phosphorylation as a novel pharmacological target to realize the therapeutic potential of increased ARNT transactivation activity.
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Affiliation(s)
- Gunsmaa Nyamsuren
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | - Gregor Rapp
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | - Hassan Dihazi
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | - Elisabeth M Zeisberg
- Department of Cardiology and Pneumology, Göttingen University Medical Center, Georg August University, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Robert Koch Street 40, Göttingen, Germany
| | - Desiree Tampe
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany
| | - Björn Tampe
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany.
| | - Michael Zeisberg
- Department of Nephrology and Rheumatology, Göttingen University Medical Center, Georg August University, Göttingen, Germany. .,German Center for Cardiovascular Research (DZHK), Robert Koch Street 40, Göttingen, Germany.
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9
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Xu X, Dikiy I, Evans MR, Marcelino LP, Gardner KH. Fragile protein folds: Sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:63-76. [PMID: 35603043 PMCID: PMC9119131 DOI: 10.5194/mr-2-63-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent research on fold-switching metamorphic proteins has revealed some notable exceptions to Anfinsen's hypothesis of protein folding. We have previously described how a single point mutation can enable a well-folded protein domain, one of the two PAS (Per-ARNT-Sim) domains of the human ARNT (aryl hydrocarbon receptor nuclear translocator) protein, to interconvert between two conformers related by a slip of an internal β-strand. Using this protein as a test case, we advance the concept of a "fragile fold," a protein fold that can reversibly rearrange into another fold that differs by a substantial number of hydrogen bonds, entailing reorganization of single secondary structure elements to more drastic changes seen in metamorphic proteins. Here we use a battery of biophysical tests to examine several factors affecting the equilibrium between the two conformations of the switching ARNT PAS-B Y456T protein. Of note, we find that factors which impact the HI loop preceding the shifted Iβ-strand affect both the equilibrium levels of the two conformers and the denatured state which links them in the interconversion process. Finally, we describe small molecules that selectively bind to and stabilize the wildtype conformation of ARNT PAS-B. These studies form a toolkit for studying fragile protein folds and could enable ways to modulate the biological functions of such fragile folds, both in natural and engineered proteins.
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Affiliation(s)
- Xingjian Xu
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA
- Ph.D. Program in Biochemistry, The Graduate Center, CUNY, New York, NY, USA
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA
- Current address: Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Matthew R Evans
- Current address: Acclaim Physician Group, Inc. Fort Worth, TX, USA
| | - Leandro P Marcelino
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, USA
- Biochemistry, Chemistry and Biology Ph.D. Programs, The Graduate Center, CUNY, New York, NY, USA
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10
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Dasgupta A, Wu D, Tian L, Xiong PY, Dunham-Snary KJ, Chen KH, Alizadeh E, Motamed M, Potus F, Hindmarch CCT, Archer SL. Mitochondria in the Pulmonary Vasculature in Health and Disease: Oxygen-Sensing, Metabolism, and Dynamics. Compr Physiol 2020; 10:713-765. [PMID: 32163206 DOI: 10.1002/cphy.c190027] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In lung vascular cells, mitochondria serve a canonical metabolic role, governing energy homeostasis. In addition, mitochondria exist in dynamic networks, which serve noncanonical functions, including regulation of redox signaling, cell cycle, apoptosis, and mitochondrial quality control. Mitochondria in pulmonary artery smooth muscle cells (PASMC) are oxygen sensors and initiate hypoxic pulmonary vasoconstriction. Acquired dysfunction of mitochondrial metabolism and dynamics contribute to a cancer-like phenotype in pulmonary arterial hypertension (PAH). Acquired mitochondrial abnormalities, such as increased pyruvate dehydrogenase kinase (PDK) and pyruvate kinase muscle isoform 2 (PKM2) expression, which increase uncoupled glycolysis (the Warburg phenomenon), are implicated in PAH. Warburg metabolism sustains energy homeostasis by the inhibition of oxidative metabolism that reduces mitochondrial apoptosis, allowing unchecked cell accumulation. Warburg metabolism is initiated by the induction of a pseudohypoxic state, in which DNA methyltransferase (DNMT)-mediated changes in redox signaling cause normoxic activation of HIF-1α and increase PDK expression. Furthermore, mitochondrial division is coordinated with nuclear division through a process called mitotic fission. Increased mitotic fission in PAH, driven by increased fission and reduced fusion favors rapid cell cycle progression and apoptosis resistance. Downregulation of the mitochondrial calcium uniporter complex (MCUC) occurs in PAH and is one potential unifying mechanism linking Warburg metabolism and mitochondrial fission. Mitochondrial metabolic and dynamic disorders combine to promote the hyperproliferative, apoptosis-resistant, phenotype in PAH PASMC, endothelial cells, and fibroblasts. Understanding the molecular mechanism regulating mitochondrial metabolism and dynamics has permitted identification of new biomarkers, nuclear and CT imaging modalities, and new therapeutic targets for PAH. © 2020 American Physiological Society. Compr Physiol 10:713-765, 2020.
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Affiliation(s)
- Asish Dasgupta
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Danchen Wu
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Lian Tian
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Ping Yu Xiong
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | | | - Kuang-Hueih Chen
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Elahe Alizadeh
- Department of Medicine, Queen's Cardiopulmonary Unit (QCPU), Translational Institute of Medicine (TIME), Queen's University, Kingston, Ontario, Canada
| | - Mehras Motamed
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - François Potus
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Charles C T Hindmarch
- Department of Medicine, Queen's Cardiopulmonary Unit (QCPU), Translational Institute of Medicine (TIME), Queen's University, Kingston, Ontario, Canada
| | - Stephen L Archer
- Department of Medicine, Queen's University, Kingston, Ontario, Canada.,Kingston Health Sciences Centre, Kingston, Ontario, Canada.,Providence Care Hospital, Kingston, Ontario, Canada
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11
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Soh JE, Abu N, Sagap I, Mazlan L, Yahaya A, Mustangin M, Khoo TS, Saidin S, Ishak M, Ab Mutalib NS, Jamal R. Validation of immunogenic PASD1 peptides against HLA-A*24:02 colorectal cancer. Immunotherapy 2019; 11:1205-1219. [PMID: 31478431 DOI: 10.2217/imt-2019-0073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer is the third commonest malignancy in Asia including Malaysia. The immunogenic cancer-testis antigens, which are expressed in a variety of cancers but with limited expression in normal tissues except the testis, represent an attractive approach to improve treatment options for colorectal cancer. We aimed to validate four PASD1 peptides as the immunotherapeutic targets in colorectal cancer. First, PASD1 mRNA and protein expression were determined via real-time polymerase chain reaction (RT-PCR) and immunohistochemistry. The PASD1 peptides specific to HLA-A*24:02 were investigated using IFN-y-ELISpot assay, followed by the cytolytic and granzyme-B-ELISpot assays to analyze the cytolytic effects of CD8+ T cells. Gene and protein expressions of PASD1 were detected in 20% and 17.3% of colorectal cancer samples, respectively. PASD1(4) peptide was shown to be immunogenic in colorectal cancer samples. CD8+ T cells raised against PASD1(4) peptide were able to lyze HLA-A*24:02+ PASD1+ cells. Our results reveal that PASD1(4) peptide represents a potential target for colorectal cancer.
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Affiliation(s)
- Joanne Ec Soh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ismail Sagap
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Luqman Mazlan
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Azyani Yahaya
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Muaatamarulain Mustangin
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Tze S Khoo
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Sazuita Saidin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Muhiddin Ishak
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nurul S Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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12
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Abstract
Cells respond to hypoxia by shifting cellular processes from general housekeeping functions to activating specialized hypoxia-response pathways. Oxygen plays an important role in generating ATP to maintain a productive rate of protein synthesis in normoxia. In hypoxia, the rate of the canonical protein synthesis pathway is significantly slowed and impaired due to limited ATP availability, necessitating an alternative mechanism to mediate protein synthesis and facilitate adaptation. Hypoxia adaptation is largely mediated by hypoxia-inducible factors (HIFs). While HIFs are well known for their transcriptional functions, they also play imperative roles in translation to mediate hypoxic protein synthesis. Such adaptations to hypoxia are often hyperactive in solid tumors, contributing to the expression of cancer hallmarks, including treatment resistance. The current literature on protein synthesis in hypoxia is reviewed here, inclusive of hypoxia-specific mRNA selection to translation termination. Current HIF targeting therapies are also discussed as are the opportunities involved with targeting hypoxia specific protein synthesis pathways.
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Affiliation(s)
- Nancy T Chee
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Ines Lohse
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Shaun P Brothers
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA.
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13
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Vignali PDA, Barbi J, Pan F. Metabolic Regulation of T Cell Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1011:87-130. [DOI: 10.1007/978-94-024-1170-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Bogdanovski DA, DiFazio LT, Bogdanovski AK, Csóka B, Jordan GB, Paul ER, Antonioli L, Pilip SA, Nemeth ZH. Hypoxia-inducible-factor-1 in trauma and critical care. J Crit Care 2017; 42:207-212. [PMID: 28779702 DOI: 10.1016/j.jcrc.2017.07.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/19/2017] [Accepted: 07/11/2017] [Indexed: 12/27/2022]
Abstract
HIF-1 is a ubiquitous signaling molecule constantly expressed by the body, but is degraded during normoxic conditions. In hypoxic conditions, it persists and is active. Hypoxia is often associated with trauma due to interrupted blood flow, inflammation or other reasons, causing HIF-1 to be active in signaling and recovery. In this review, the function of HIF-1 is examined, as well as its clinical significance with regard to trauma and critical care. Using this information, we then identify potential points of treatment and intervention.
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Affiliation(s)
| | | | | | - Balázs Csóka
- Dept. of Surgery, Rutgers-New Jersey Medical School, United States.
| | | | - Elina R Paul
- Dept. of Surgery, Morristown Medical Center, United States.
| | - Luca Antonioli
- Dept. of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
| | | | - Zoltan H Nemeth
- Dept. of Surgery, Morristown Medical Center, United States; Dept. of Surgery, Rutgers-New Jersey Medical School, United States.
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15
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Curcumin mediates anticancer effects by modulating multiple cell signaling pathways. Clin Sci (Lond) 2017; 131:1781-1799. [PMID: 28679846 DOI: 10.1042/cs20160935] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/05/2017] [Accepted: 04/21/2017] [Indexed: 12/18/2022]
Abstract
Curcumin, a component of a spice native to India, was first isolated in 1815 by Vogel and Pelletier from the rhizomes of Curcuma longa (turmeric) and, subsequently, the chemical structure of curcumin as diferuloylmethane was reported by Milobedzka et al. [(1910) 43., 2163-2170]. Since then, this polyphenol has been shown to exhibit antioxidant, anti-inflammatory, anticancer, antiviral, antibacterial, and antifungal activities. The current review primarily focuses on the anticancer potential of curcumin through the modulation of multiple cell signaling pathways. Curcumin modulates diverse transcription factors, inflammatory cytokines, enzymes, kinases, growth factors, receptors, and various other proteins with an affinity ranging from the pM to the mM range. Furthermore, curcumin effectively regulates tumor cell growth via modulation of numerous cell signaling pathways and potentiates the effect of chemotherapeutic agents and radiation against cancer. Curcumin can interact with most of the targets that are modulated by FDA-approved drugs for cancer therapy. The focus of this review is to discuss the molecular basis for the anticancer activities of curcumin based on preclinical and clinical findings.
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16
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Schulte KW, Green E, Wilz A, Platten M, Daumke O. Structural Basis for Aryl Hydrocarbon Receptor-Mediated Gene Activation. Structure 2017; 25:1025-1033.e3. [PMID: 28602820 DOI: 10.1016/j.str.2017.05.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 12/15/2022]
Abstract
The aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) constitute a heterodimeric basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain containing transcription factor with central functions in development and cellular homeostasis. AHR is activated by xenobiotics, notably dioxin, as well as by exogenous and endogenous metabolites. Modulation of AHR activity holds promise for the treatment of diseases featuring altered cellular homeostasis, such as cancer or autoimmune disorders. Here, we present the crystal structure of a heterodimeric AHR:ARNT complex containing the PAS A and bHLH domain bound to its target DNA. The structure provides insights into the DNA binding mode of AHR and elucidates how stable dimerization of AHR:ARNT is achieved through sophisticated domain interplay via three specific interfaces. Using mutational analyses, we prove the relevance of the observed interfaces for AHR-mediated gene activation. Thus, our work establishes the structural basis of AHR assembly and DNA interaction and provides a template for targeted drug design.
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Affiliation(s)
- Kathrin Wiebke Schulte
- Crystallography Department, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Edward Green
- Department of Neurology, University Hospital Heidelberg and National Center for Tumor Diseases, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Annabel Wilz
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Platten
- Department of Neurology, University Hospital Heidelberg and National Center for Tumor Diseases, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Neurology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany.
| | - Oliver Daumke
- Crystallography Department, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.
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17
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Cui XG, Han ZT, He SH, Wu XD, Chen TR, Shao CH, Chen DL, Su N, Chen YM, Wang T, Wang J, Song DW, Yan WJ, Yang XH, Liu T, Wei HF, Xiao J. HIF1/2α mediates hypoxia-induced LDHA expression in human pancreatic cancer cells. Oncotarget 2017; 8:24840-24852. [PMID: 28193910 PMCID: PMC5421893 DOI: 10.18632/oncotarget.15266] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 12/15/2016] [Indexed: 01/16/2023] Open
Abstract
Glycolysis is a typical conduit for energy metabolism in pancreatic cancer (PC) due to the hypoxic microenviroment. Lactate dehydrogenase A (LDHA) catalyzes the conversion of pyruvate to lactate and is considered to be a key checkpoint of anaerobic glycolysis. The aim of the present study was to explore the mechanism of interactions between hypoxia, HIF-1/2α and LDHA, and the function of LDHA on PC cells by analyzing 244 PC and paratumor specimens. It was found that LDHA was over-expressed and related to tumor stages. The result of in vitro study demonstrated that hypoxia induced LDHA expression. To explore the relationship between HIF and LDHA, chromatin immunoprecipitation assay and luciferase assay were performed. The result showed that HIF-1/2α bound to LDHA at 89bp under the hypoxic condition. Furthermore, knockdown of endogenous HIF-1α and HIF-2α decreased the LDHA expression even in the hypoxic condition, which was accompanied with a significant decrease in lactate production and glucose utilization (p < 0.01). Immunofluorescence in the 244 specimens showed that HIF-1/2α was over-expressed and associated with LDHA over-expression (p < 0.0001). Forced expression of LDHA promoted the growth and migration of PC cells, while knocking down the expression of LDHA inhibited the cell growth and migration markedly. In summary, the present study proved that HIF1/2α could activate LDHA expression in human PC cells, and high expression of LDHA promoted the growth and migration of PC cells.
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Affiliation(s)
- Xin-gang Cui
- Department of Urinary Surgery of Third Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Zhi-tao Han
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Department of Spine Surgery, Ruikang Hospital, Guangxi University Of Chinese Medicine, Guangxi, China
| | - Shao-hui He
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xing-da Wu
- Department of Pancreatic Surgery, the First Hospital of China Medical University, Shenyang, China
| | - Tian-rui Chen
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Cheng-hao Shao
- Department of Pancreatic Surgery, Changzheng Hospital, the Second Military Medical University, Shanghai, China
| | - Dan-lei Chen
- Department of Pancreatic Surgery, Changzheng Hospital, the Second Military Medical University, Shanghai, China
| | - Ning Su
- Department of Colorectal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yuan-ming Chen
- Department of Spine Surgery, Ruikang Hospital, Guangxi University Of Chinese Medicine, Guangxi, China
| | - Ting Wang
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jing Wang
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Dian-Wen Song
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wang-jun Yan
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xing-Hai Yang
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Tielong Liu
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hai-feng Wei
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jianru Xiao
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
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18
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Inamoto I, Chen G, Shin JA. The DNA target determines the dimerization partner selected by bHLHZ-like hybrid proteins AhRJun and ArntFos. MOLECULAR BIOSYSTEMS 2017; 13:476-488. [DOI: 10.1039/c6mb00795c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The molecular basis of protein–partner selection and DNA binding of the basic helix–loop–helix (bHLH) and basic region-leucine zipper (bZIP) superfamilies of dimeric transcription factors is fundamental toward understanding gene regulation.
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Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry
- University of Toronto
- Mississauga
- Canada L5L 1C6
| | - Gang Chen
- Department of Chemistry
- University of Toronto
- Mississauga
- Canada L5L 1C6
| | - Jumi A. Shin
- Department of Chemistry
- University of Toronto
- Mississauga
- Canada L5L 1C6
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19
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Xue T, Song C, Wang Q, Wang Y, Chen G. Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study. PLoS One 2016; 11:e0155105. [PMID: 27153104 PMCID: PMC4859532 DOI: 10.1371/journal.pone.0155105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/25/2016] [Indexed: 11/18/2022] Open
Abstract
The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA combination of the CLOCK and BMAL1 proteins play a key role in the positive and negative transcriptional feedback processes. In the present work, we constructed a series of binary and ternary models for the bHLH/bHLH-PAS domains of the CLOCK and BMAL1 proteins, and the DNA molecule, and carried out molecular dynamics simulations, free energy calculations and conformational analysis to explore the interaction properties of the CLOCK and BMAL1 proteins with DNA. The results show that the bHLH domains of CLOCK and BMAL1 can favorably form the heterodimer of the bHLH domains of CLOCK and BMAL1 and the homodimer of the bHLH domains of BMAL1. And both dimers could respectively bind to DNA at its H1-H1 interface. The DNA bindings of the H1 helices in the hetero- and homo-bHLH dimers present the rectangular and diagonal binding modes, respectively. Due to the function of the α-helical forceps in these dimers, the tight gripping of the H1 helices to the major groove of DNA would cause the decrease of interactions at the H1-H2 interfaces in the CLOCK and BMAL1 proteins. The additional PAS domains in the CLOCK and BMAL1 proteins affect insignificantly the interactions of the CLOCK and BMAL1 proteins with the DNA molecule due to the flexible and long loop linkers located at the middle of the PAS and bHLH domains. The present work theoretically explains the interaction mechanisms of the bHLH domains of the CLOCK and BMAL1 proteins with DNA.
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Affiliation(s)
- Tuo Xue
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Chunnian Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Qing Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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20
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Wilkins SE, Abboud MI, Hancock RL, Schofield CJ. Targeting Protein-Protein Interactions in the HIF System. ChemMedChem 2016; 11:773-86. [PMID: 26997519 PMCID: PMC4848768 DOI: 10.1002/cmdc.201600012] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/24/2016] [Indexed: 12/18/2022]
Abstract
Animals respond to chronic hypoxia by increasing the levels of a transcription factor known as the hypoxia-inducible factor (HIF). HIF upregulates multiple genes, the products of which work to ameliorate the effects of limited oxygen at cellular and systemic levels. Hypoxia sensing by the HIF system involves hydroxylase-catalysed post-translational modifications of the HIF α-subunits, which 1) signal for degradation of HIF-α and 2) limit binding of HIF to transcriptional coactivator proteins. Because the hypoxic response is relevant to multiple disease states, therapeutic manipulation of the HIF-mediated response has considerable medicinal potential. In addition to modulation of catalysis by the HIF hydroxylases, the HIF system manifests other possibilities for therapeutic intervention involving protein-protein and protein-nucleic acid interactions. Recent advances in our understanding of the structural biology and biochemistry of the HIF system are facilitating medicinal chemistry efforts. Herein we give an overview of the HIF system, focusing on structural knowledge of protein-protein interactions and how this might be used to modulate the hypoxic response for therapeutic benefit.
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Affiliation(s)
- Sarah E Wilkins
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rebecca L Hancock
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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21
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Yoshii K, Tajima F, Ishijima S, Sagami I. Changes in pH and NADPH regulate the DNA binding activity of neuronal PAS domain protein 2, a mammalian circadian transcription factor. Biochemistry 2015; 54:250-9. [PMID: 25526362 DOI: 10.1021/bi5008518] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Neuronal PAS domain protein 2 (NPAS2) is a core clock transcription factor that forms a heterodimer with BMAL1 to bind the E-box in the promoter of clock genes and is regulated by various environmental stimuli such as heme, carbon monoxide, and NAD(P)H. In this study, we investigated the effects of pH and NADPH on the DNA binding activity of NPAS2. In an electrophoretic mobility shift (EMS) assay, the pH of the reaction mixture affected the DNA binding activity of the NPAS2/BMAL1 heterodimer but not that of the BMAL1/BMAL1 homodimer. A change in pH from 7.0 to 7.5 resulted in a 1.7-fold increase in activity in the absence of NADPH, and NADPH additively enhanced the activity up to 2.7-fold at pH 7.5. The experiments using truncated mutants revealed that N-terminal amino acids 1-61 of NPAS2 were sufficient to sense the change in both pH and NADPH. We further analyzed the kinetics of formation and DNA binding of the NPAS2/BMAL1 heterodimer at various pH values. In the absence of NADPH, a change in pH from 6.5 to 8.0 decreased the KD(app) value of the E-box from 125 to 22 nM, with an 8-fold increase in the maximal level of DNA binding for the NPAS2/BMAL1 heterodimer. The addition of NADPH resulted in a further decrease in KD(app) to 9 nM at pH 8.0. Furthermore, NPAS2-dependent transcriptional activity in a luciferase assay using NIH3T3 cells also increased with the pH of the culture medium. These results suggest that NPAS2 has a role as a pH and metabolite sensor in regulating circadian rhythms.
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Affiliation(s)
- Katsuhiro Yoshii
- Graduate School of Life and Environmental Science, Kyoto Prefectural University , Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
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22
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Characterization of human variants in obesity-related SIM1 protein identifies a hot-spot for dimerization with the partner protein ARNT2. Biochem J 2014; 461:403-12. [DOI: 10.1042/bj20131618] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Several non-synonymous variants found in obese patients disrupt function of the transcription factor SIM1 (single-minded 1) by impairing binding to an essential partner protein. The clustering of these variants reveals a mutational hot-spot critical for function of SIM1 and the related protein SIM2.
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23
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Reitzel AM, Karchner SI, Franks DG, Evans BR, Nacci D, Champlin D, Vieira VM, Hahn ME. Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats. BMC Evol Biol 2014; 14:6. [PMID: 24422594 PMCID: PMC3899389 DOI: 10.1186/1471-2148-14-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/18/2013] [Indexed: 11/27/2022] Open
Abstract
Background The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other “dioxin-like compounds” (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and evidence for positive selection at three AHR-related loci (AHR1, AHR2, AHRR) in F. heteroclitus by comparing alleles from seven locations ranging over 600 km along the northeastern US, including extremely polluted and reference estuaries, with a focus on New Bedford Harbor (MA, USA), a PCB Superfund site, and nearby reference sites. Results We identified 98 single nucleotide polymorphisms within three AHR-related loci among all populations, including synonymous and nonsynonymous substitutions. Haplotype distributions were spatially segregated and F-statistics suggested strong population genetic structure at these loci, consistent with previous studies showing strong population genetic structure at other F. heteroclitus loci. Genetic diversity at these three loci was not significantly different in contaminated sites as compared to reference sites. However, for AHR2 the New Bedford Harbor population had significant FST values in comparison to the nearest reference populations. Tests for positive selection revealed ten nonsynonymous polymorphisms in AHR1 and four in AHR2. Four nonsynonymous SNPs in AHR1 and three in AHR2 showed large differences in base frequency between New Bedford Harbor and its reference site. Tests for isolation-by-distance revealed evidence for non-neutral change at the AHR2 locus. Conclusion Together, these data suggest that F. heteroclitus populations in reference and polluted sites have similar genetic diversity, providing no evidence for strong genetic bottlenecks for populations in polluted locations. However, the data provide evidence for genetic differentiation among sites, selection at specific nucleotides in AHR1 and AHR2, and specific AHR2 SNPs and haplotypes that are associated with the PCB-resistant phenotype in the New Bedford Harbor population. The results suggest that AHRs, and especially AHR2, may be important, recurring targets for selection in local adaptation to dioxin-like aromatic hydrocarbon contaminants.
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Affiliation(s)
| | | | | | | | | | | | | | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02568, USA.
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24
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Ramachandrappa S, Raimondo A, Cali AM, Keogh JM, Henning E, Saeed S, Thompson A, Garg S, Bochukova EG, Brage S, Trowse V, Wheeler E, Sullivan AE, Dattani M, Clayton PE, Datta V, Bruning JB, Wareham NJ, O’Rahilly S, Peet DJ, Barroso I, Whitelaw ML, Farooqi IS, Farooqi IS. Rare variants in single-minded 1 (SIM1) are associated with severe obesity. J Clin Invest 2013; 123:3042-50. [PMID: 23778139 PMCID: PMC3696558 DOI: 10.1172/jci68016] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/18/2013] [Indexed: 02/02/2023] Open
Abstract
Single-minded 1 (SIM1) is a basic helix-loop-helix transcription factor involved in the development and function of the paraventricular nucleus of the hypothalamus. Obesity has been reported in Sim1 haploinsufficient mice and in a patient with a balanced translocation disrupting SIM1. We sequenced the coding region of SIM1 in 2,100 patients with severe, early onset obesity and in 1,680 controls. Thirteen different heterozygous variants in SIM1 were identified in 28 unrelated severely obese patients. Nine of the 13 variants significantly reduced the ability of SIM1 to activate a SIM1-responsive reporter gene when studied in stably transfected cells coexpressing the heterodimeric partners of SIM1 (ARNT or ARNT2). SIM1 variants with reduced activity cosegregated with obesity in extended family studies with variable penetrance. We studied the phenotype of patients carrying variants that exhibited reduced activity in vitro. Variant carriers exhibited increased ad libitum food intake at a test meal, normal basal metabolic rate, and evidence of autonomic dysfunction. Eleven of the 13 probands had evidence of a neurobehavioral phenotype. The phenotypic similarities between patients with SIM1 deficiency and melanocortin 4 receptor (MC4R) deficiency suggest that some of the effects of SIM1 deficiency on energy homeostasis are mediated by altered melanocortin signaling.
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Affiliation(s)
- Shwetha Ramachandrappa
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Anne Raimondo
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Anna M.G. Cali
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Julia M. Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Sadia Saeed
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Amanda Thompson
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Sumedha Garg
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Elena G. Bochukova
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Soren Brage
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Victoria Trowse
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Eleanor Wheeler
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Adrienne E. Sullivan
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Mehul Dattani
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Peter E. Clayton
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Vippan Datta
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - John B. Bruning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Nick J. Wareham
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Stephen O’Rahilly
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Daniel J. Peet
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Ines Barroso
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - Murray L. Whitelaw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Discipline of Biochemistry, School of Molecular and Biomedical Science and Australian Research Council Special Research Centre for the Molecular Genetics of Development, University of Adelaide, Adelaide, Australia.
Wellcome Trust Sanger Institute, Cambridge, United Kingdom.
MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom.
Clinical and Molecular Genetics Unit, University College London Institute of Child Health, London, United Kingdom.
Manchester Academic Health Sciences Centre, Royal Manchester Children’s Hospital, Manchester, United Kingdom.
Norfolk and Norwich University Hospital NHS Foundation Trust, Norwich, United Kingdom
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Lyberopoulou A, Mylonis I, Papachristos G, Sagris D, Kalousi A, Befani C, Liakos P, Simos G, Georgatsou E. MgcRacGAP, a cytoskeleton regulator, inhibits HIF-1 transcriptional activity by blocking its dimerization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1378-87. [PMID: 23458834 DOI: 10.1016/j.bbamcr.2013.02.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 02/19/2013] [Accepted: 02/21/2013] [Indexed: 01/22/2023]
Abstract
Hypoxia inducible factor-1 (HIF-1), a dimeric transcription factor of the bHLH-PAS family, is comprised of HIF-1α, which is inducible by hypoxia and ARNT or HIF-1β, which is constitutively expressed. HIF-1 is involved in cellular homeostasis under hypoxia, in development and in several diseases affected by oxygen availability, particularly cancer. Since its expression is positively correlated with poor outcome prognosis for cancer patients, HIF-1 is a target for pharmaceutical therapy. We have previously shown that male germ cell Rac GTPase activating protein (MgcRacGAP), a regulator of Rho proteins which are principally involved in cytoskeletal organization, binds to HIF-1α and inhibits its transcriptional activity. In this work, we have explored the mechanism of the MgcRacGAP-mediated HIF-1 inactivation. We show that the Myo domain of MgcRacGAP, which is both necessary and sufficient for HIF-1 repression, binds to the PAS-B domain of HIF-1α. Furthermore MgcRacGAP competes with ARNT for binding to the HIF-1α PAS-B domain, as shown by in vitro binding pull down assays. In mammalian cells, ARNT overexpression can overcome the MgcRacGAP-mediated inhibition and MgcRacGAP binding to HIF-1α in vivo inhibits its dimerization with ARNT. We additionally present results indicating that MgcRacGAP binding to HIF-1α is specific, since it does not affect the transcriptional activity of HIF-2, a close evolutionary relative of HIF-1 also involved in hypoxia regulation and cancer. Our results reveal a new mechanism for HIF-1 transcriptional activity regulation, suggest a novel hypoxia-cytoskeleton link and provide new tools for selective HIF-1 inhibition.
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26
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Chen G, De Jong AT, Shin JA. Forced homodimerization of the c-Fos leucine zipper in designed bHLHZ-like hybrid proteins MaxbHLH-Fos and ArntbHLH-Fos. MOLECULAR BIOSYSTEMS 2012; 8:1286-96. [DOI: 10.1039/c2mb05354c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Urban JD, Budinsky RA, Rowlands JC. Single nucleotide polymorphisms in the human aryl hydrocarbon receptor nuclear translocator (ARNT) gene. Drug Metab Pharmacokinet 2011; 26:637-45. [PMID: 21828933 DOI: 10.2133/dmpk.dmpk-11-sc-031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Species' variation(s) in gene homologues can result in differences among species in their quantitative and qualitative susceptibility and responsiveness to environmental contaminants. In the case of dioxin-like compounds (DLCs), it has been hypothesized that single nucleotide polymorphisms (SNPs) in genes associated with aryl hydrocarbon receptor (AHR)-regulated pathways may result in greater susceptibility to DLC toxicity. A key step in the activation of AHR involves heterodimerization with the AHR nuclear translocator (ARNT) protein before binding to its DNA response element. The objective of this study was to identify SNPs in the human ARNT gene that could potentially affect the sensitivity of AHR-dependent gene transcription. Results from DNA sequencing of 101 human samples demonstrated the presence of five unique SNPs at the ARNT locus, including three non-synonymous SNPs, of which two were novel: V304M and T462A. The genetic frequencies of the non-synonymous SNPs were very low (≤0.02), and the novel SNPs occurred in the Per-ARNT-Sim (PAS) functional domain. In silico analysis indicated that V304M was the only SNP identified in the current population with the potential to significantly alter ARNT protein function. Our findings indicated a very limited occurrence of SNPs with predicted functional consequence in key domains of human ARNT.
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28
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Xue Y, Li NL, Yang JY, Chen Y, Yang LL, Liu WC. Phosphatidylinositol 3′-kinase signaling pathway is essential for Rac1-induced hypoxia-inducible factor-1α and vascular endothelial growth factor expression. Am J Physiol Heart Circ Physiol 2011; 300:H2169-76. [DOI: 10.1152/ajpheart.00970.2010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have previously demonstrated the roles of RhoA, Rac1, and Cdc42 in hypoxia-driven angiogenesis. However, the role of oncogenes in hypoxia signaling is poorly understood. Given the importance of Rho proteins in the hypoxic response, we hypothesized that Rho family members could act as mediators of hypoxic signal transduction. We investigated the cross-talk between hypoxia and oncogene-driven signal transduction pathways and explored the role of Rac1 on hypoxia-induced hypoxia-inducible factor (HIF)-1α and VEGF expression. Since the phosphatidylinositol 3′-kinase (PI3K) pathway is involved in signal transduction of many oncogenes, we explored the role of PI3K on Rac1-mediated expression of HIF-1α and VEGF in hypoxia. We showed that LY-294002, a PI3K inhibitor, suppressed HIF-1α and VEGF induction under hypoxic conditions by up to 50%. Activation of Rac1 resulted in an upregulation of hypoxia-induced HIF-1α expression, which was blocked by LY-294002. These data suggested that Rac1 is an intermediate in the PI3K-mediated induction of HIF-1α. Interestingly, there was a significant downregulation of the tumor suppressor genes p53 and von Hippel-Lindau tumor suppressor (VHL) in cells expressing a constitutively active form of Rac1. Rac1-mediated inhibition of p53 and VHL could therefore be implicated in the upregulation of HIF-1α expression.
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Affiliation(s)
- Yan Xue
- Departments of 1Clinical Oncology and
| | - Nan-Lin Li
- Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | | | - Yan Chen
- Departments of 1Clinical Oncology and
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Coactivators necessary for transcriptional output of the hypoxia inducible factor, HIF, are directly recruited by ARNT PAS-B. Proc Natl Acad Sci U S A 2011; 108:7739-44. [PMID: 21512126 DOI: 10.1073/pnas.1101357108] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hypoxia-inducible factor (HIF) is the key transcriptional effector of the hypoxia response in eukaryotes, coordinating the expression of genes involved in oxygen transport, glycolysis, and angiogenesis to promote adaptation to low oxygen levels. HIF is a basic helix-loop-helix (bHLH)-PAS (PER-ARNT-SIM) heterodimer composed of an oxygen-labile HIF-α subunit and a constitutively expressed aryl hydrocarbon receptor nuclear translocator (ARNT) subunit, which dimerize via basic helix-loop-helix and PAS domains, and recruit coactivators via HIF-α C-terminal transactivation domains. Here we demonstrate that the ARNT PAS-B domain provides an additional recruitment site by binding the coactivator transforming acidic coiled-coil 3 (TACC3) in a step necessary for transcriptional responses to hypoxia. Structural insights from NMR spectroscopy illustrate how this PAS domain simultaneously mediates interactions with HIF-α and TACC3. Finally, mutations on ARNT PAS-B modulate coactivator selectivity and target gene induction by HIF in vivo, demonstrating a bifunctional role for transcriptional regulation by PAS domains within bHLH-PAS transcription factors.
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30
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Hao N, Whitelaw ML, Shearwin KE, Dodd IB, Chapman-Smith A. Identification of residues in the N-terminal PAS domains important for dimerization of Arnt and AhR. Nucleic Acids Res 2011; 39:3695-709. [PMID: 21245039 PMCID: PMC3089468 DOI: 10.1093/nar/gkq1336] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The basic helix–loop–helix (bHLH).PAS dimeric transcription factors have crucial roles in development, stress response, oxygen homeostasis and neurogenesis. Their target gene specificity depends in part on partner protein choices, where dimerization with common partner Aryl hydrocarbon receptor nuclear translocator (Arnt) is an essential step towards forming active, DNA binding complexes. Using a new bacterial two-hybrid system that selects for loss of protein interactions, we have identified 22 amino acids in the N-terminal PAS domain of Arnt that are involved in heterodimerization with aryl hydrocarbon receptor (AhR). Of these, Arnt E163 and Arnt S190 were selective for the AhR/Arnt interaction, since mutations at these positions had little effect on Arnt dimerization with other bHLH.PAS partners, while substitution of Arnt D217 affected the interaction with both AhR and hypoxia inducible factor-1α but not with single minded 1 and 2 or neuronal PAS4. Arnt uses the same face of the N-terminal PAS domain for homo- and heterodimerization and mutational analysis of AhR demonstrated that the equivalent region is used by AhR when dimerizing with Arnt. These interfaces differ from the PAS β-scaffold surfaces used for dimerization between the C-terminal PAS domains of hypoxia inducible factor-2α and Arnt, commonly used for PAS domain interactions.
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Affiliation(s)
- Nan Hao
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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31
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Scheu PD, Kim OB, Griesinger C, Unden G. Sensing by the membrane-bound sensor kinase DcuS: exogenous versus endogenous sensing of C4-dicarboxylates in bacteria. Future Microbiol 2010; 5:1383-402. [DOI: 10.2217/fmb.10.103] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bacteria are able to grow at the expense of both common (succinate, L-malate, fumarate and aspartate) and uncommon (L-tartrate and D-malate) C4-dicarboxylates, which are components of central metabolism. Two types of sensors/regulators responding to the C4-dicarboxylates function in Escherichia coli, Bacillus, Lactobacillus and related bacteria. The first type represents membrane-integral two-component systems, while the second includes cytoplasmic LysR-type transcriptional regulators. The difference in location and substrate specificity allows the exogenous induction of metabolic genes by common C4-dicarboxylates, and endogenous induction by uncommon C4-dicarboxylates. The two-component sensors, DcuS and CitA, are composed of an extracellular Per-Arnt-Sim (PAS) domain, two transmembrane helices, a cytoplasmic PAS and the kinase domain. The structures of the extracellular PAS domains of DcuS and CitA have been determined in the ligand-bound and the apo form. Binding of the ligand results in closing and compaction of the binding site, and the structural change gives rise to piston-type movement of the adjacent membrane-spanning helix-2, and signal transmission to the cytoplasmic side. For DcuS, a membrane-embedded construct has been developed that suggests (by experimentation and modeling) that plasticity of the cytoplasmic PAS domain is central to signal transduction from the membrane to the kinase. Sensor kinase DcuS of E. coli requires the C4-dicarboxylate transporters DctA or DcuB as co-sensors for function under aerobic and anaerobic conditions, respectively. DcuB contains a regulatory site that controls the function of DcuS and is independent from the transport region. Therefore, DcuS senses C4-dicarboxylates in two independent modes, responding to the effector concentration and the metabolic flux of extracellular C4-dicarboxylates.
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Affiliation(s)
- Patrick D Scheu
- Institute for Microbiology & Wine Research, University of Mainz, 55099 Mainz, Germany
| | - Ok Bin Kim
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Christian Griesinger
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-Based Structural Biology, Göttingen, Germany
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32
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Kalousi A, Mylonis I, Politou AS, Chachami G, Paraskeva E, Simos G. Casein kinase 1 regulates human hypoxia-inducible factor HIF-1. J Cell Sci 2010; 123:2976-86. [PMID: 20699359 DOI: 10.1242/jcs.068122] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hypoxia-inducible factor 1 (HIF-1), a transcriptional activator that mediates cellular response to hypoxia and a promising target of anticancer therapy, is essential for adaptation to low oxygen conditions, embryogenesis and tumor progression. HIF-1 is a heterodimer of HIF-1alpha, expression of which is controlled by oxygen levels as well as by various oxygen-independent mechanisms, and HIF-1beta (or ARNT), which is constitutively expressed. In this work, we investigate the phosphorylation of the N-terminal heterodimerization (PAS) domain of HIF-1alpha and identify Ser247 as a major site of in vitro modification by casein kinase 1delta (CK1delta). Mutation of this site to alanine, surprisingly, enhanced the transcriptional activity of HIF-1alpha, a result phenocopied by inhibition or small interfering RNA (siRNA)-mediated silencing of CK1delta under hypoxic conditions. Conversely, overexpression of CK1delta or phosphomimetic mutation of Ser247 to aspartate inhibited HIF-1alpha activity without affecting its stability or nuclear accumulation. Immunoprecipitation and in vitro binding experiments suggest that CK1-dependent phosphorylation of HIF-1alpha at Ser247 impairs its association with ARNT, a notion also supported by modeling the structure of the complex between HIF-1alpha and ARNT PAS-B domains. We suggest that modification of HIF-1alpha by CK1 represents a novel mechanism that controls the activity of HIF-1 during hypoxia by regulating the interaction between its two subunits.
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Affiliation(s)
- Alkmini Kalousi
- Laboratory of Biochemistry, School of Medicine, University of Thessaly, Mezourlo 41110, Larissa, Greece
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33
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McIntosh BE, Hogenesch JB, Bradfield CA. Mammalian Per-Arnt-Sim proteins in environmental adaptation. Annu Rev Physiol 2010; 72:625-45. [PMID: 20148691 DOI: 10.1146/annurev-physiol-021909-135922] [Citation(s) in RCA: 265] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Per-Arnt-Sim (PAS) domain is conserved across the kingdoms of life and found in an ever-growing list of proteins. This domain can bind to and sense endogenous or xenobiotic small molecules such as molecular oxygen, cellular metabolites, or polyaromatic hydrocarbons. Members of this family are often found in pathways that regulate responses to environmental change; in mammals these include the hypoxia, circadian, and dioxin response pathways. These pathways function in development and throughout life to regulate cellular, organ, and whole-organism adaptive responses. Remarkably, in the case of the clock, this adaptation includes anticipation of environmental change. In this review, we summarize the roles of PAS domain-containing proteins in mammals. We provide structural evidence that functionally classifies both known and unknown biological roles. Finally, we discuss the role of PAS proteins in anticipation of and adaptation to environmental change.
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Affiliation(s)
- Brian E McIntosh
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.
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Podar K, Anderson KC. A therapeutic role for targeting c-Myc/Hif-1-dependent signaling pathways. Cell Cycle 2010; 9:1722-8. [PMID: 20404562 DOI: 10.4161/cc.9.9.11358] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Deregulated c-Myc occurs in approximately 30% of human cancers. Similarly, hypoxia-inducible factor (HIF) is commonly overexpressed in a variety of human malignancies. Under physiologic conditions, HIF inhibits c-Myc activity; however, when deregulated oncogenic c-Myc collaborates with HIF in inducing the expression of VEGF, PDK1 and hexokinase 2. Most of the knowledge of HIF derives from studies investigating a role of HIF under hypoxic conditions, however, HIF-1alpha stabilization is also found in normoxic conditions. Specifically, under hypoxic conditions HIF-1-mediated regulation of oncogenic c-Myc plays a pivotal role in conferring metabolic advantages to tumor cells as well as adaptation to the tumorigenic micromilieu. In addition, our own results show that under normoxic conditions oncogenic c-Myc is required for constitutive high HIF-1 protein levels and activity in Multiple Myeloma (MM) cells, thereby influencing VEGF secretion and angiogenic activity within the bone marrow microenvironment. Further studies are needed to delineate the functional relevance of HIF, MYC, and the HIF-MYC collaboration in MM and other malignancies, also integrating the tumor microenvironment and the cellular context. Importantly, early studies already demonstrate promising preclinical of novel agents, predominantly small molecules, which target c-Myc, HIF or both.
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Affiliation(s)
- Klaus Podar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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35
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Xu J, De Jong AT, Chen G, Chow HK, Damaso CO, Schwartz Mittelman A, Shin JA. Reengineering natural design by rational design and in vivo library selection: the HLH subdomain in bHLHZ proteins is a unique requirement for DNA-binding function. Protein Eng Des Sel 2010; 23:337-46. [PMID: 20086039 DOI: 10.1093/protein/gzp082] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To explore the role of the HLH subdomain in bHLHZ proteins, we designed sets of minimalist proteins based on bHLHZ protein Max, bHLH/PAS protein Arnt and bZIP protein C/EBP. In the first, the Max bHLH and C/EBP leucine zipper were fused such that the leucine heptad repeats were not in register; therefore, the protein dimerization interface was disrupted. Max1bHLH-C/EBP showed little ability to activate transcription from the E-box (5'-CACGTG) in the yeast one-hybrid assay, and no E-box binding by quantitative fluorescence anisotropy. Max1bHLH-C/EBP's activity was significantly improved after library selection (three amino acids randomized between HLH and leucine zipper), despite the Max bHLH and C/EBP zipper still being out of register: a representative mutant gave a high nanomolar K(d) value for E-box binding. Thus, selection proved to be a powerful tool for salvaging the flawed Max1bHLH-C/EBP, although the out-of-register mutants still did not achieve the strong DNA-binding affinities displayed by their in-register counterparts. ArntbHLH-C/EBP hybrids further demonstrated the importance of maintaining register, as out-of-register mutants showed no E-box-responsive activity, whereas the in-register hybrid showed moderate activity. In another design, we eliminated the HLH altogether and fused the Max basic region to the C/EBP zipper to generate bZIP-like hybrids. Despite numerous designs and selections, these hybrids possessed no E-box-responsive activity. Finally, we tested the importance of the loop sequence in MaxbHLHZ by fluorescence and circular dichroism. In one mutant, the loop was shortened by two residues; in the other, the Lys57:DNA-backbone interaction was abolished by mutation to Gly57. Both showed markedly decreased E-box-binding relative to MaxbHLHZ. Our results suggest that, in contrast to the more rigid bZIP, the HLH is capable of significant conformational adaptation to enable gene-regulatory function and is required for protein dimerization and positioning the basic region for DNA recognition.
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Affiliation(s)
- Jing Xu
- Department of Chemistry, University of Toronto, Mississauga, ON L5L1C6, Canada
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36
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Furness SGB, Whelan F. The pleiotropy of dioxin toxicity--xenobiotic misappropriation of the aryl hydrocarbon receptor's alternative physiological roles. Pharmacol Ther 2009; 124:336-53. [PMID: 19781569 DOI: 10.1016/j.pharmthera.2009.09.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 10/20/2022]
Abstract
The aryl hydrocarbon receptor is a signal regulated transcription factor that has best been characterised as regulating the xenobiotic response to a variety of planar aromatic hydrocarbons. There is compelling evidence that it mediates most, if not all, of the toxic effects of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin). Dioxin exposure results in a wide variety of toxic outcomes including severe wasting syndrome, chloracne, thymic involution, severe immune suppression, reduced fertility, hepatotoxicity, teratogenicity, tumour promotion and death. The pleiotropy of toxic outcomes implies the disruption of a wide range of normal physiological functions. The aryl hydrocarbon receptor has developmentally restricted expression as well as developmental defects in gene-targeted mice. It has a wide range of target genes that do not fit into the classical xenobiotic metabolising gene battery and has recently been shown to interact with NF-kappa B and the estrogen receptor. There is also evidence for its activation in the absence of exogenous ligand, all of which point to various roles outside xenobiotic metabolism. Ligands so far identified display differential activation potential with respect to receptor activity. This article addresses activities of the aryl hydrocarbon receptor that are outside the xenobiotic response. Known physiological roles are discussed as well as how their disruption contributes to the pleiotropic toxicity of TCDD.
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Affiliation(s)
- Sebastian G B Furness
- Drug Discovery Biology Laboratory, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.
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37
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The active form of human aryl hydrocarbon receptor (AHR) repressor lacks exon 8, and its Pro 185 and Ala 185 variants repress both AHR and hypoxia-inducible factor. Mol Cell Biol 2009; 29:3465-77. [PMID: 19380484 DOI: 10.1128/mcb.00206-09] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The aryl hydrocarbon receptor (AHR) repressor (AHRR) inhibits AHR-mediated transcription and has been associated with reproductive dysfunction and tumorigenesis in humans. Previous studies have characterized the repressor function of AHRRs from mice and fish, but the human AHRR ortholog (AHRR(715)) appeared to be nonfunctional in vitro. Here, we report a novel human AHRR cDNA (AHRRDelta8) that lacks exon 8 of AHRR(715). AHRRDelta8 was the predominant AHRR form expressed in human tissues and cell lines. AHRRDelta8 effectively repressed AHR-dependent transactivation, whereas AHRR(715) was much less active. Similarly, AHRRDelta8, but not AHRR(715), formed a complex with AHR nuclear translocator (ARNT). Repression of AHR by AHRRDelta8 was not relieved by overexpression of ARNT or AHR coactivators, suggesting that competition for these cofactors is not the mechanism of repression. AHRRDelta8 interacted weakly with AHR but did not inhibit its nuclear translocation. In a survey of transcription factor specificity, AHRRDelta8 did not repress the nuclear receptor pregnane X receptor or estrogen receptor alpha but did repress hypoxia-inducible factor (HIF)-dependent signaling. AHRRDelta8-Pro(185) and -Ala(185) variants, which have been linked to human reproductive disorders, both were capable of repressing AHR or HIF. Together, these results identify AHRRDelta8 as the active form of human AHRR and reveal novel aspects of its function and specificity as a repressor.
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38
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Partch CL, Card PB, Amezcua CA, Gardner KH. Molecular basis of coiled coil coactivator recruitment by the aryl hydrocarbon receptor nuclear translocator (ARNT). J Biol Chem 2009; 284:15184-92. [PMID: 19324882 DOI: 10.1074/jbc.m808479200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aryl hydrocarbon receptor nuclear translocator (ARNT) serves as the obligate heterodimeric partner for bHLH-PAS proteins involved in sensing and coordinating transcriptional responses to xenobiotics, hypoxia, and developmental pathways. Although its C-terminal transactivation domain is dispensable for transcriptional activation in vivo, ARNT has recently been shown to use its N-terminal bHLH and/or PAS domains to interact with several transcriptional coactivators that are required for transcriptional initiation after xenobiotic or hypoxic cues. Here we show that ARNT uses a single PAS domain to interact with two coiled coil coactivators, TRIP230 and CoCoA. Both coactivators interact with the same interface on the ARNT PAS-B domain, located on the opposite side of the domain used to associate with the analogous PAS domain on its heterodimeric bHLH-PAS partner HIF-2alpha. Using NMR and biochemical studies, we identified the ARNT-interacting motif of one coactivator, TRIP230 as an LXXLL-like nuclear receptor box. Mutation of this motif and proximal sequences disrupts the interaction with ARNT PAS-B. Identification of this ARNT-coactivator interface illustrates how ARNT PAS-B is used to form critical interactions with both bHLH-PAS partners and coactivators that are required for transcriptional responses.
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Affiliation(s)
- Carrie L Partch
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
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39
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Adams JM, Difazio LT, Rolandelli RH, Luján JJ, Haskó G, Csóka B, Selmeczy Z, Németh ZH. HIF-1: a key mediator in hypoxia. ACTA ACUST UNITED AC 2009; 96:19-28. [PMID: 19264039 DOI: 10.1556/aphysiol.96.2009.1.2] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The transcription factor HIF-1 is one of the principal mediators of homeostasis in human tissues exposed to hypoxia. It is implicated in virtually every process of rapid gene expression in response to low oxygen levels. The most common causes of tissue hypoxia are inflammation and/or insufficient circulation or a combination of both. Inflamed tissues and the areas surrounding malignant tumors are characterized by hypoxia and low concentrations of glucose. Serious and generalized inflammation can lead to sepsis and circulatory collapse resulting in acute or chronic tissue hypoxia in various vital organs which induces a rapid homeostatic process in all nucleated cells of affected organs in the human body. Under hypoxic conditions the alpha and beta subunits of HIF-1 make an active heterodimer and drive the transcription of over 60 genes important for cell survival, adaptation, anaerobic metabolism, immune reaction, cytokine production, vascularization and general tissue homeostasis. In addition, HIF-1 plays a key role in the development of physiological systems in fetal and postnatal life. It is also a critical mediator of cancer, lung and cardiovascular diseases. The better understanding of the functions of HIF-1 and the pharmacological modulation of its activity could mean a successful therapeutic approach to these diseases.
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Affiliation(s)
- J M Adams
- Department of Surgery, Morristown Memorial Hospital, Morristown, NJ 07960, USA
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40
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ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space. Proc Natl Acad Sci U S A 2009; 106:2617-22. [PMID: 19196990 DOI: 10.1073/pnas.0808270106] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The aryl hydrocarbon receptor nuclear translocator (ARNT) is a basic helix-loop-helix Period/ARNT/Single-minded (bHLH-PAS) protein that controls various biological pathways as part of dimeric transcriptional regulator complexes with other bHLH-PAS proteins. The two PAS domains within ARNT, PAS-A and PAS-B, are essential for the formation of these complexes because they mediate protein-protein interactions via residues located on their beta-sheet surfaces. While investigating the importance of residues in ARNT PAS-B involved in these interactions, we uncovered a point mutation (Y456T) on the solvent-exposed beta-sheet surface that allowed this domain to interconvert with a second, stable conformation. Although both conformations are present in equivalent quantities in the Y456T mutant, this can be shifted almost completely to either end point by additional mutations. A high-resolution solution structure of a mutant ARNT PAS-B domain stabilized in the new conformation revealed a 3-residue slip in register and accompanying inversion of the central Ibeta-strand. We have demonstrated that the new conformation has >100-fold lower in vitro affinity for its heterodimerization partner, hypoxia-inducible factor 2alpha PAS-B. We speculate that the pliability in beta-strand register is related to the flexibility required of ARNT to bind to several partners and, more broadly, to the abilities of some PAS domains to regulate their activities in response to small-molecule cofactors.
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41
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Soshilov A, Denison MS. Role of the Per/Arnt/Sim domains in ligand-dependent transformation of the aryl hydrocarbon receptor. J Biol Chem 2008; 283:32995-3005. [PMID: 18806268 PMCID: PMC2583286 DOI: 10.1074/jbc.m802414200] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 08/21/2008] [Indexed: 11/06/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) mediates the toxic and biological effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin and related compounds. In a process termed transformation, ligand binding converts the AhR into its high affinity DNA binding form that represents a dimer of the AhR and Arnt, a closely related nuclear protein. During transformation, protein chaperone Hsp90 is thought to be replaced by Arnt in overlapping binding sites in the basic helix loop helix and PASB domains of the AhR. Here, analysis of AhR variants containing a modified PASB domain and AhR PASA-PASB fragments of various lengths revealed (i) an inhibitory effect on transformation concomitant with Hsp90 binding in the PASB domain, (ii) an ability of the PASA-PASB fragment of the AhR to reproduce key steps in the transformation process, and (iii) a ligand-dependent conformational change in the PASA domain consistent with increased PASA exposure during AhR transformation. Based on these results, we propose a new mechanism of AhR transformation through initiation of Arnt dimerization and Hsp90 displacement in AhR PASA/B domains. This study provides insights into mechanisms of AhR transformation, dimerization of PAS domain proteins, and Hsp90 dissociation in activation of its client proteins.
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Affiliation(s)
- Anatoly Soshilov
- Department of Environmental Toxicology, University of California, Davis, California 95616, USA
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42
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Chow HK, Xu J, Shahravan SH, De Jong AT, Chen G, Shin JA. Hybrids of the bHLH and bZIP protein motifs display different DNA-binding activities in vivo vs. in vitro. PLoS One 2008; 3:e3514. [PMID: 18949049 PMCID: PMC2568859 DOI: 10.1371/journal.pone.0003514] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/02/2008] [Indexed: 12/18/2022] Open
Abstract
Minimalist hybrids comprising the DNA-binding domain of bHLH/PAS (basic-helix-loop-helix/Per-Arnt-Sim) protein Arnt fused to the leucine zipper (LZ) dimerization domain from bZIP (basic region-leucine zipper) protein C/EBP were designed to bind the E-box DNA site, CACGTG, targeted by bHLHZ (basic-helix-loop-helix-zipper) proteins Myc and Max, as well as the Arnt homodimer. The bHLHZ-like structure of ArntbHLH-C/EBP comprises the Arnt bHLH domain fused to the C/EBP LZ: i.e. swap of the 330 aa PAS domain for the 29 aa LZ. In the yeast one-hybrid assay (Y1H), transcriptional activation from the E-box was strong by ArntbHLH-C/EBP, and undetectable for the truncated ArntbHLH (PAS removed), as detected via readout from the HIS3 and lacZ reporters. In contrast, fluorescence anisotropy titrations showed affinities for the E-box with ArntbHLH-C/EBP and ArntbHLH comparable to other transcription factors (K(d) 148.9 nM and 40.2 nM, respectively), but only under select conditions that maintained folded protein. Although in vivo yeast results and in vitro spectroscopic studies for ArntbHLH-C/EBP targeting the E-box correlate well, the same does not hold for ArntbHLH. As circular dichroism confirms that ArntbHLH-C/EBP is a much more strongly alpha-helical structure than ArntbHLH, we conclude that the nonfunctional ArntbHLH in the Y1H must be due to misfolding, leading to the false negative that this protein is incapable of targeting the E-box. Many experiments, including protein design and selections from large libraries, depend on protein domains remaining well-behaved in the nonnative experimental environment, especially small motifs like the bHLH (60-70 aa). Interestingly, a short helical LZ can serve as a folding- and/or solubility-enhancing tag, an important device given the focus of current research on exploration of vast networks of biomolecular interactions.
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Affiliation(s)
- Hiu-Kwan Chow
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Jing Xu
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - S. Hesam Shahravan
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Antonia T. De Jong
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Gang Chen
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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Woods S, Farrall A, Procko C, Whitelaw ML. The bHLH/Per-Arnt-Sim transcription factor SIM2 regulates muscle transcript myomesin2 via a novel, non-canonical E-box sequence. Nucleic Acids Res 2008; 36:3716-27. [PMID: 18480125 PMCID: PMC2441813 DOI: 10.1093/nar/gkn247] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite a growing number of descriptive studies that show Single-minded 2 (Sim2) is not only essential for murine survival, but also upregulated in colon, prostate and pancreatic tumours, there is a lack of direct target genes identified for this basic helix-loop-helix/PAS transcription factor. We have performed a set of microarray experiments aimed at identifying genes that are differentially regulated by SIM2, and successfully verified that the Myomesin2 (Myom2) gene is SIM2-responsive. Although SIM2 has been reported to be a transcription repressor, we find that SIM2 induces transcription of Myom2 and activates the Myom2 promoter sequence when co-expressed with the heterodimeric partner protein, ARNT1, in human embryonic kidney cells. Truncation and mutation of the Myom2 promoter sequence, combined with chromatin immunoprecipitation studies in cells, has lead to the delineation of a non-canonical E-box sequence 5'-AACGTG-3' that is bound by SIM2/ARNT1 heterodimers. Interestingly, in immortalized human myoblasts knock down of Sim2 results in increased levels of Myom2 RNA, suggesting that SIM2 is acting as a repressor in these cells and so its activity is likely to be highly context dependent. This is the first report of a direct SIM2/ARNT1 target gene with accompanying analysis of a functional response element.
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Affiliation(s)
- Susan Woods
- School of Molecular & Biomedical Science (Biochemistry) and the Centre for the Molecular Genetics of Development, University of Adelaide, South Australia 5005, Australia.
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44
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Pattanaik S, Xie CH, Yuan L. The interaction domains of the plant Myc-like bHLH transcription factors can regulate the transactivation strength. PLANTA 2008; 227:707-15. [PMID: 18075757 DOI: 10.1007/s00425-007-0676-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 12/01/2007] [Indexed: 05/03/2023]
Abstract
The N-terminal region of the plant Myc-like basic helix-loop-helix transcription factors (bHLH TFs) contains two domains. Approximately, 190 amino acids at the N-terminus comprise an interaction domain, a.k.a. Myb-interacting-region (MIR) for its primary function of interacting with Myb-like TFs. Following, the interaction domain is an activation (or acidic) domain responsible for transactivation. We have previously discovered that a lysine to methionine substitution (K157M) in the interaction domain of Myc-RP of Perilla frutescens leads to a 50-fold increase in transactivation activity. The result suggests that mutations in the interaction domain affect transactivation. The highly conserved nature of this lysine residue in many Myc-like bHLH TFs prompted us to explore the functional importance of this residue within the TF family and the influence of the interaction domain on the activation domain in transactivation. We found that the replacement of the equivalent lysine with methionine significantly affects the transactivation activities of two other Myc-RP homologues, Delila from snapdragon and Lc from maize. In addition to methionine, substitution with several other amino acids at this position has positive effects on transcriptional activity. A neighboring conserved alanine residue (A159 in Myc-RP, A161 in Delila and A172 in Lc) also affects transactivation. Substitution of this alanine residue to an aspartic acid abolished transactivation of both Myc-RP and Delila and severely reduced transactivation of Lc. Ectopic expression of a Myc-RP K157M mutant in transgenic tobacco resulted in increased anthocyanin accumulation compared to plants expressing the wild-type gene. Our study reveals the potential cooperation between functional domains of the bHLH TFs.
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Affiliation(s)
- Sitakanta Pattanaik
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, Lexington, Cooper and University Drives, KY 40546, USA
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45
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Dougherty EJ, Pollenz RS. Analysis of Ah receptor-ARNT and Ah receptor-ARNT2 complexes in vitro and in cell culture. Toxicol Sci 2007; 103:191-206. [PMID: 18096572 DOI: 10.1093/toxsci/kfm300] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
ARNT and ARNT2 proteins are expressed in mammalian and aquatic species and exhibit a high level of amino acid identity in the basic-helix loop-helix PER/ARNT/SIM domains involved in protein interactions and DNA binding. Since the analysis of ARNT2 function at the protein level has been limited, ARNT2 function in aryl hydrocarbon receptor (AHR)-mediated signaling was evaluated and compared to ARNT. In vitro, ARNT and ARNT2 dimerized equally with the AHR in the presence of 2,3,7,8-tetracholorodibenzo-p-dioxin (TCDD) and ARNT2 outcompeted ARNT for binding to the AHR when expressed in excess. In contrast, activation of the AHR with 3-methylcholanthrene or benzo[a]pyrene resulted in predominant formation of AHR*ARNT complexes. ARNT2 expressed in Hepa-1 cell culture lines with reduced ARNT protein resulted in minimal induction of endogenous CYP1A1 protein compared to cells expressing ARNT, and mutation of the putative proline residue at amino acid 352 to histidine failed to produce an ARNT2 that could function in AHR-mediated signaling. However, the expression of ARNT2 in wild-type Hepa-1 cells reduced TCDD-mediated induction of endogenous CYP1A1 protein by 30%, even though AHR*ARNT2 complexes could not be detected in nuclear extracts. Western blot analysis of numerous mouse tissues and various cell culture lines showed that both endogenous ARNT and ARNT2 could be detected in cells derived from kidney, central nervous system, and retinal epithelium. Thus, ARNT2 has the ability to dimerize with the liganded AHR in vitro and is influenced by the activating ligand yet appears to be limited in its ability to influence AHR-mediated signaling in cell culture.
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Affiliation(s)
- Edward J Dougherty
- Division of Cell Biology, Microbiology, and Molecular Biology, Department of Biology, University of South Florida, Tampa, Florida 33620, USA
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46
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Evans BR, Karchner SI, Allan LL, Pollenz RS, Tanguay RL, Jenny MJ, Sherr DH, Hahn ME. Repression of aryl hydrocarbon receptor (AHR) signaling by AHR repressor: role of DNA binding and competition for AHR nuclear translocator. Mol Pharmacol 2007; 73:387-98. [PMID: 18000031 DOI: 10.1124/mol.107.040204] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzo-p-dioxin causes altered gene expression and toxicity. The AHR repressor (AHRR) inhibits AHR signaling through a proposed mechanism involving competition with AHR for dimerization with AHR nuclear translocator (ARNT) and binding to AHR-responsive enhancer elements (AHREs). We sought to delineate the relative roles of competition for ARNT and AHREs in the mechanism of repression. In transient transfections in which AHR2-dependent transactivation was repressed by AHRR1 or AHRR2, increasing ARNT expression failed to reverse the repression, suggesting that AHRR inhibition of AHR signaling does not occur through sequestration of ARNT. An AHRR1 point mutant (AHRR1-Y9F) that could not bind to AHREs but that retained its nuclear localization was only slightly reduced in its ability to repress AHR2, demonstrating that AHRR repression does not occur solely through competition for AHREs. When both proposed mechanisms were blocked (AHRR1-Y9F plus excess ARNT), AHRR remained functional. AHRR1 neither blocked AHR nuclear translocation nor reduced the levels of AHR2 protein. Experiments using AHRR1 C-terminal deletion mutants showed that amino acids 270 to 550 are dispensable for repression. These results demonstrate that repression of AHR transactivation by AHRR involves the N-terminal portion of AHRR; does not involve competition for ARNT; and does not require binding to AHREs, although AHRE binding can contribute to the repression. We propose a mechanism of AHRR action involving "transrepression" of AHR signaling through protein-protein interactions rather than by inhibition of the formation or DNA binding of the AHR-ARNT complex.
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Affiliation(s)
- Brad R Evans
- Department of Biology, MS#32, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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47
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Yucel MA, Kurnaz IA. An in silico model for HIF-alpha regulation and hypoxia response in tumor cells. Biotechnol Bioeng 2007; 97:588-600. [PMID: 17089387 DOI: 10.1002/bit.21247] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The dependency of the growth and metastasis of tumors on the new blood vessel formation, or angiogenesis, has opened up new potentials to tumor therapy, nevertheless understanding the molecular mechanisms involved in angiogenesis is crucial in the bioengineering of novel anti-angiogenic drugs. The key component in hypoxia sensing in tumor cells is the hypoxia-inducible factor, HIF-1alpha, which is inactivated through proteosome-mediated degradation under normoxic conditions. Two enzymes have been reported to hydroxylate HIF-1alpha, namely prolyl hydroxylase (PH), recruiting the proetasome complex and degrading cytoplasmic HIF-1alpha, and asparaginyl hydroxylase/factor inhibiting HIF-1alpha (FIH-1), downregulating the recruitment of p300 to the promoter, thereby reducing the transcriptional activity of HIF-1alpha. In this study, we have constructed an in silico model of a tumor cell using the GEPASI 3.30 biochemical simulation software (http://www.gepasi.org) and studied the performances of PH and FIH-1 on HIF-1alpha degradation and inactivation, respectively, as monitored by expression of the vascular endothelial growth factor, VEGF, during hypoxia. In our biochemical models, FIH-1 can successfully increase hypoxic transcription of VEGF, however FIH-1 on its own is not sufficient to inactivate HIF-1 completely, leading to background VEGF transcription under normoxic conditions. On the other hand, PH is necessary to increase the hypoxic transcriptional response, and can effectively shut off normoxic transcription. We therefore propose that regulating PH activity can be a primary target for anti-angiogenic bioengineering research.
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Affiliation(s)
- Meryem A Yucel
- Bogazici University, Institute of Biomedical Engineering, Bebek, Istanbul, Turkey
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Furness SGB, Lees MJ, Whitelaw ML. The dioxin (aryl hydrocarbon) receptor as a model for adaptive responses of bHLH/PAS transcription factors. FEBS Lett 2007; 581:3616-25. [PMID: 17459381 DOI: 10.1016/j.febslet.2007.04.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 04/03/2007] [Accepted: 04/04/2007] [Indexed: 11/19/2022]
Abstract
This review examines the common theme of adaptive responses of bHLH/PAS proteins, using the dioxin receptor as a prototype. The bHLH/PAS family of transcriptional regulators are a group of key developmental and environmental stress sensing proteins. They employ a variety of post-translational control mechanisms to regulate their transcriptional output. Amongst this family, the dioxin receptor is best known for its ability to elicit toxic responses to dioxin and dioxin like chemicals even though it mediates more benign adaptive responses to non-toxic xenobiotics. We discuss what is known about dioxin receptor physiology, both adaptive and inherent, along with its molecular regulation and put this into the context of the wider bHLH/PAS family. We also raise the issue of its toxic responses, in particular the idea that it is the dysregulation of its poorly characterised housekeeping functions that leads to these outcomes.
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Affiliation(s)
- Sebastian G B Furness
- Drug Discovery Laboratory, Department of Pharmacology, Building 13E, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.
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Scheuermann TH, Yang J, Zhang L, Gardner KH, Bruick RK. Hypoxia-inducible factors Per/ARNT/Sim domains: structure and function. Methods Enzymol 2007; 435:3-24. [PMID: 17998046 DOI: 10.1016/s0076-6879(07)35001-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hypoxia-inducible factors (HIFs) are key transcriptional regulators of genes involved in cellular adaptation to reduced oxygen availability through effects on anaerobic metabolism, oxygen delivery, angiogenesis, and cellular survival and proliferation. As such, HIFs contribute to the pathogenesis of diseases in which oxygen availability is compromised, notably ischemia and tumorigenesis. Though tremendous progress has been made in elucidating the mechanisms underlying O(2)-dependent regulation of HIF by Fe(II)- and 2-oxoglutarate-dependent dioxygenases, HIF induction can be uncoupled from these modes of regulation in diseases such as cancer. Consequently, renewed interest has developed in understanding the structure/function relationships of individual P(er)/ARNT/S(im) (PAS) domains that are important for maintaining transcriptionally active HIF complexes, regardless of the manner by which HIF is induced. This review highlights strategies for the biophysical and biochemical characterization of the PAS domains found within both HIF subunits and provides a platform for future efforts to exploit these domains in therapeutic settings.
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Affiliation(s)
- Thomas H Scheuermann
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Yamamoto T, Kyo M, Kamiya T, Tanaka T, Engel JD, Motohashi H, Yamamoto M. Predictive base substitution rules that determine the binding and transcriptional specificity of Maf recognition elements. Genes Cells 2006; 11:575-91. [PMID: 16716189 DOI: 10.1111/j.1365-2443.2006.00965.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Small Maf transcription factors possess a basic region-leucine zipper motif through which they form homodimers or heterodimers with CNC and Bach proteins. Different combinations of small Maf and CNC/Bach protein dimers bind to cis-acting DNA elements, collectively referred to as Maf-recognition elements (MAREs), to either activate or repress transcription. As MAREs defined by function are often divergent from the consensus sequence, we speculated that sequence variations in the MAREs form the basis for selective Maf:Maf or Maf:CNC dimer binding. To test this hypothesis, we analyzed the binding of Maf-containing dimers to variant sequences of the MARE using bacterially expressed MafG and Nrf2 proteins and a surface plasmon resonance-microarray imaging technique. We found that base substitutions in the MAREs actually determined their binding preference for different dimers. In fact, we were able to categorize MAREs into five groups: MafG homodimer-orientd MAREs (Groups I and II), ambivalent MAREs (Group III), MafG:Nrf2 heterodimer-orientd MAREs (Group IV), and silent MAREs (Group V). This study thus manifests that a clear set of rules pertaining to the cis-acting element determine whether a given MARE preferentially associates with MafG homodimer or with MafG:Nrf2 heterodimer.
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Affiliation(s)
- Tae Yamamoto
- Graduate School of Comprehensive Human Sciences and Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577, Japan
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