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Gálvez-Navas JM, Molina-Montes E, Rodríguez-Barranco M, Ramírez-Tortosa MC, Gil Á, Sánchez MJ. Molecular Mechanisms Linking Genes and Vitamins of the Complex B Related to One-Carbon Metabolism in Breast Cancer: An In Silico Functional Database Study. Int J Mol Sci 2024; 25:8175. [PMID: 39125744 PMCID: PMC11311893 DOI: 10.3390/ijms25158175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Carcinogenesis is closely related to the expression, maintenance, and stability of DNA. These processes are regulated by one-carbon metabolism (1CM), which involves several vitamins of the complex B (folate, B2, B6, and B12), whereas alcohol disrupts the cycle due to the inhibition of folate activity. The relationship between nutrients related to 1CM (all aforementioned vitamins and alcohol) in breast cancer has been reviewed. The interplay of genes related to 1CM was also analyzed. Single nucleotide polymorphisms located in those genes were selected by considering the minor allele frequency in the Caucasian population and the linkage disequilibrium. These genes were used to perform several in silico functional analyses (considering corrected p-values < 0.05 as statistically significant) using various tools (FUMA, ShinyGO, and REVIGO) and databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and GeneOntology (GO). The results of this study showed that intake of 1CM-related B-complex vitamins is key to preventing breast cancer development and survival. Also, the genes involved in 1CM are overexpressed in mammary breast tissue and participate in a wide variety of biological phenomena related to cancer. Moreover, these genes are involved in alterations that give rise to several types of neoplasms, including breast cancer. Thus, this study supports the role of one-carbon metabolism B-complex vitamins and genes in breast cancer; the interaction between both should be addressed in future studies.
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Affiliation(s)
- José María Gálvez-Navas
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.M.G.-N.); (M.-J.S.)
- Cancer Registry of Granada, Andalusian School of Public Health, Campus Universitario de Cartuja, Cuesta del Observatorio 4, 18011 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Av. de Madrid, 18012 Granada, Spain;
- Ph.D. Program in Nutrition and Food Sciences, International Postgraduate School, University of Granada, Av. de Madrid 13, 18012 Granada, Spain
| | - Esther Molina-Montes
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.M.G.-N.); (M.-J.S.)
- Instituto de Investigación Biosanitaria ibs. GRANADA, Av. de Madrid, 18012 Granada, Spain;
- Department of Nutrition and Food Sciences, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18011 Granada, Spain
| | - Miguel Rodríguez-Barranco
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.M.G.-N.); (M.-J.S.)
- Cancer Registry of Granada, Andalusian School of Public Health, Campus Universitario de Cartuja, Cuesta del Observatorio 4, 18011 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Av. de Madrid, 18012 Granada, Spain;
| | - MCarmen Ramírez-Tortosa
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18011 Granada, Spain;
| | - Ángel Gil
- Instituto de Investigación Biosanitaria ibs. GRANADA, Av. de Madrid, 18012 Granada, Spain;
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18011 Granada, Spain;
- Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición (CIBEROBN), 28029 Madrid, Spain
| | - María-José Sánchez
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain; (J.M.G.-N.); (M.-J.S.)
- Cancer Registry of Granada, Andalusian School of Public Health, Campus Universitario de Cartuja, Cuesta del Observatorio 4, 18011 Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Av. de Madrid, 18012 Granada, Spain;
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2
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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3
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Li TZ, Bai CY, Wu B, Zhang CY, Wang WT, Shi TW, Zhou J. The Elk-3 target Abhd10 ameliorates hepatotoxic injury and fibrosis in alcoholic liver disease. Commun Biol 2023; 6:682. [PMID: 37400491 DOI: 10.1038/s42003-023-05055-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 06/19/2023] [Indexed: 07/05/2023] Open
Abstract
Alcoholic liver disease (ALD) and other forms of chronic hepatotoxic injury can lead to transforming growth factor β1 (TGFβ1)-induced hepatic fibrosis and compromised liver function, underscoring the need to develop novel treatments for these conditions. Herein, our analyses of liver tissue samples from severe alcoholic hepatitis (SAH) patients and two murine models of ALD reveals that the ALD phenotype was associated with upregulation of the transcription factor ETS domain-containing protein (ELK-3) and ELK-3 signaling activity coupled with downregulation of α/β hydrolase domain containing 10 (ABHD10) and upregulation of deactivating S-palmitoylation of the antioxidant protein Peroxiredoxin 5 (PRDX5). In vitro, we further demonstrate that ELK-3 can directly bind to the ABHD10 promoter to inhibit its transactivation. TGFβ1 and epidermal growth factor (EGF) signaling induce ABHD10 downregulation and PRDX5 S-palmitoylation via ELK-3. This ELK-3-mediated ABHD10 downregulation drives oxidative stress and disrupts mature hepatocyte function via enhancing S-palmitoylation of PRDX5's Cys100 residue. In vivo, ectopic Abhd10 overexpression ameliorates liver damage in ALD model mice. Overall, these data suggest that the therapeutic targeting of the ABHD10-PRDX5 axis may represent a viable approach to treating ALD and other forms of hepatotoxicity.
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Affiliation(s)
- Tian-Zhu Li
- Department of Molecular Biology, College of Basic Medical Science, Chifeng University, Chifeng, 024000, China.
| | - Chun-Ying Bai
- Department of Molecular Biology, College of Basic Medical Science, Chifeng University, Chifeng, 024000, China
| | - Bao Wu
- Department of Tissue and Embryology, College of Basic Medical Science, Chifeng University, Chifeng, 024000, China
| | - Cong-Ying Zhang
- Department of Pharmacy, College of Basic Medical Science, Chifeng University, Chifeng, 024000, China
| | - Wen-Tao Wang
- Department of Pathogenic Biology, College of Basic Medical Science, Chifeng University, Chifeng, 024000, China
| | - Tie-Wei Shi
- Department of Molecular Biology, College of Basic Medical Science, Chifeng University, Chifeng, 024000, China
| | - Jing Zhou
- Department of Molecular Biology, College of Basic Medical Science, Chifeng University, Chifeng, 024000, China
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4
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Mikami Y, Grubb BR, Rogers TD, Dang H, Asakura T, Kota P, Gilmore RC, Okuda K, Morton LC, Sun L, Chen G, Wykoff JA, Ehre C, Vilar J, van Heusden C, Livraghi-Butrico A, Gentzsch M, Button B, Stutts MJ, Randell SH, O’Neal WK, Boucher RC. Chronic airway epithelial hypoxia exacerbates injury in muco-obstructive lung disease through mucus hyperconcentration. Sci Transl Med 2023; 15:eabo7728. [PMID: 37285404 PMCID: PMC10664029 DOI: 10.1126/scitranslmed.abo7728] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
Unlike solid organs, human airway epithelia derive their oxygen from inspired air rather than the vasculature. Many pulmonary diseases are associated with intraluminal airway obstruction caused by aspirated foreign bodies, virus infection, tumors, or mucus plugs intrinsic to airway disease, including cystic fibrosis (CF). Consistent with requirements for luminal O2, airway epithelia surrounding mucus plugs in chronic obstructive pulmonary disease (COPD) lungs are hypoxic. Despite these observations, the effects of chronic hypoxia (CH) on airway epithelial host defense functions relevant to pulmonary disease have not been investigated. Molecular characterization of resected human lungs from individuals with a spectrum of muco-obstructive lung diseases (MOLDs) or COVID-19 identified molecular features of chronic hypoxia, including increased EGLN3 expression, in epithelia lining mucus-obstructed airways. In vitro experiments using cultured chronically hypoxic airway epithelia revealed conversion to a glycolytic metabolic state with maintenance of cellular architecture. Chronically hypoxic airway epithelia unexpectedly exhibited increased MUC5B mucin production and increased transepithelial Na+ and fluid absorption mediated by HIF1α/HIF2α-dependent up-regulation of β and γENaC (epithelial Na+ channel) subunit expression. The combination of increased Na+ absorption and MUC5B production generated hyperconcentrated mucus predicted to perpetuate obstruction. Single-cell and bulk RNA sequencing analyses of chronically hypoxic cultured airway epithelia revealed transcriptional changes involved in airway wall remodeling, destruction, and angiogenesis. These results were confirmed by RNA-in situ hybridization studies of lungs from individuals with MOLD. Our data suggest that chronic airway epithelial hypoxia may be central to the pathogenesis of persistent mucus accumulation in MOLDs and associated airway wall damage.
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Affiliation(s)
- Yu Mikami
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Barbara R. Grubb
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Troy D. Rogers
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Takanori Asakura
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Pradeep Kota
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rodney C. Gilmore
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kenichi Okuda
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lisa C. Morton
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ling Sun
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gang Chen
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason A. Wykoff
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Camille Ehre
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Juan Vilar
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Catharina van Heusden
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Martina Gentzsch
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian Button
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - M. Jackson Stutts
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Scott H. Randell
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wanda K. O’Neal
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Richard C. Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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5
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Yan B, Wang C, Chakravorty S, Zhang Z, Kadadi SD, Zhuang Y, Sirit I, Hu Y, Jung M, Sahoo SS, Wang L, Shao K, Anderson NL, Trujillo‐Ochoa JL, Briggs SD, Liu X, Olson MR, Afzali B, Zhao B, Kazemian M. A comprehensive single cell data analysis of lymphoblastoid cells reveals the role of super-enhancers in maintaining EBV latency. J Med Virol 2023; 95:e28362. [PMID: 36453088 PMCID: PMC10027397 DOI: 10.1002/jmv.28362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022]
Abstract
We probed the lifecycle of Epstein-Barr virus (EBV) on a cell-by-cell basis using single cell RNA sequencing (scRNA-seq) data from nine publicly available lymphoblastoid cell lines (LCLs). While the majority of LCLs comprised cells containing EBV in the latent phase, two other clusters of cells were clearly evident and were distinguished by distinct expression of host and viral genes. Notably, both were high expressors of EBV LMP1/BNLF2 and BZLF1 compared to another cluster that expressed neither gene. The two novel clusters differed from each other in their expression of EBV lytic genes, including glycoprotein gene GP350. The first cluster, comprising GP350- LMP1hi cells, expressed high levels of HIF1A and was transcriptionally regulated by HIF1-α. Treatment of LCLs with Pevonedistat, a drug that enhances HIF1-α signaling, markedly induced this cluster. The second cluster, containing GP350+ LMP1hi cells, expressed EBV lytic genes. Host genes that are controlled by super-enhancers (SEs), such as transcription factors MYC and IRF4, had the lowest expression in this cluster. Functionally, the expression of genes regulated by MYC and IRF4 in GP350+ LMP1hi cells were lower compared to other cells. Indeed, induction of EBV lytic reactivation in EBV+ AKATA reduced the expression of these SE-regulated genes. Furthermore, CRISPR-mediated perturbation of the MYC or IRF4 SEs in LCLs induced the lytic EBV gene expression, suggesting that host SEs and/or SE target genes are required for maintenance of EBV latency. Collectively, our study revealed EBV-associated heterogeneity among LCLs that may have functional consequence on host and viral biology.
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Affiliation(s)
- Bingyu Yan
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
| | - Chong Wang
- Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | | | - Zonghao Zhang
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Simran D. Kadadi
- Department of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | - Yuxin Zhuang
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
| | - Isabella Sirit
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Yonghua Hu
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Minwoo Jung
- Department of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | | | - Luopin Wang
- Department of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | - Kunming Shao
- Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Nicole L. Anderson
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Jorge L. Trujillo‐Ochoa
- Immunoregulation Section, Kidney Diseases BranchNational Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIHBethesdaMarylandUSA
| | - Scott D. Briggs
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
| | - Xing Liu
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
| | - Matthew R. Olson
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases BranchNational Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIHBethesdaMarylandUSA
| | - Bo Zhao
- Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Majid Kazemian
- Department of BiochemistryPurdue UniversityWest LafayetteIndianaUSA
- Department of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
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6
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Yu X, Du C, Cui Y, Jiang Y, Feng D. ELK3 Targeting AEG1 Promotes Migration and Invasion of Ovarian Cancer Cells under Hypoxia. Biol Pharm Bull 2023; 46:883-892. [PMID: 37394639 DOI: 10.1248/bpb.b22-00780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Ovarian cancer (OC) is one of the most common tumors in female reproductive organs with a five-year survival rate of less than 45%. Metastasis is a crucial contributor to OC development. ETS transcription factor (ELK3), as a transcriptional factor, have been involved in multiple tumor development. However, its role in OC remains elusive. In this study, we observed high expression of ELK3 and AEG1 in human OC tissues. OVCAR-3 and SKOV3 cells were treated with hypoxia to mimic tumor microenvironment in vivo. We found that the expression of ELK3 was significantly increased in cells under hypoxia compared with normoxia. ELK3 knockdown inhibited cell migration and invasion abilities under hypoxia. Moreover, ELK3 knockdown decreased β-catenin expression and inhibited the activation of Wnt/β-catenin pathway in SKOV3 cells under hypoxia. Astrocyte-elevated gene-1 (AEG1) has been reported to promote OC progression. Our results showed that the mRNA level of AEG1 was decreased when ELK3 knockdown under hypoxia. Dural luciferase assay confirmed that ELK3 bound to gene AEG1 promoter (-2005-+15) and enhanced its transcriptional activity under hypoxia. Overexpression of AEG1 increased the migration and invasion abilities of SKOV3 cell with ELK3 knockdown. In the absence of ELK3, the activation of β-catenin was recovered by AEG1 overexpression. To sum up, we conclude that ELK3 promotes AEG1 expression by binding to its promoter. ELK3 could promote migration and invasion of OC cells by targeting AEG1, which provides a potential basis for therapeutic approaches to OC.
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Affiliation(s)
- Xiaoyu Yu
- Department of Pathology, Harbin Medical University Cancer Hospital
| | - Chun Du
- Department of Pathology, Harbin Medical University Cancer Hospital
| | - Yifei Cui
- Department of Pathology, Harbin Medical University Cancer Hospital
| | - Yang Jiang
- Department of Pathology, Harbin Medical University Cancer Hospital
| | - Di Feng
- Department of Pathology, Harbin Medical University Cancer Hospital
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7
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Zhao Q, Ren Y, Xie H, Yu L, Lu J, Jiang W, Xiao W, Zhu Z, Wan R, Li B. ELK3 Mediated by ZEB1 Facilitates the Growth and Metastasis of Pancreatic Carcinoma by Activating the Wnt/β-Catenin Pathway. Front Cell Dev Biol 2021; 9:700192. [PMID: 34409034 PMCID: PMC8365240 DOI: 10.3389/fcell.2021.700192] [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: 05/17/2021] [Accepted: 07/15/2021] [Indexed: 11/18/2022] Open
Abstract
Rapid progression and metastasis are the major causes of death in patients with pancreatic ductal adenocarcinoma (PDAC). ELK3, a member of the ternary complex factor (TCF), has been associated with the initiation and progression of various cancers. However, the role of ELK3 in PDAC is not yet fully understood. Online databases and immunohistochemistry were used to analyze the ELK3 levels in PDAC tissues. The function of ELK3 was confirmed by a series of in vivo and in vitro studies. Western blotting and immunofluorescence were used to detect the molecular mechanisms of PDAC. ChIP-qPCR was used to study the mechanism responsible for the elevation of ELK3 expression in PDAC. The ELK3 levels were higher in PDAC tissues than in adjacent normal tissues. Functionally, we demonstrated that ELK3 acted as an oncogene to promote PDAC tumorigenesis and metastasis. Further study suggested that ELK3 promoted PDAC cell migration and invasion by activating the Wnt/β-catenin pathway, and proved that ZEB1 could directly bind to the promoter of ELK3 to increase its transcription. Finally, both were associated with the patients’ clinicopathological features and worse overall survival. Conclusively, our findings enrich the role of ELK3 in PDAC, and provide potential avenues for exploring more effective biomarkers and therapeutic strategies for the treatment of PDAC.
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Affiliation(s)
- Qiuyan Zhao
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingchun Ren
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoran Xie
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lanting Yu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiawei Lu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiliang Jiang
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqin Xiao
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhonglin Zhu
- Department of Gastrointestinal Surgery, Henan Provincial People's Hospital, Zhengzhou, China
| | - Rong Wan
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baiwen Li
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Pancreatic Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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8
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Baroni LV, Sundaresan L, Heled A, Coltin H, Pajtler KW, Lin T, Merchant TE, McLendon R, Faria C, Buntine M, White CL, Pfister SM, Gilbert MR, Armstrong TS, Bouffet E, Kumar S, Taylor MD, Aldape KD, Ellison DW, Gottardo NG, Kool M, Korshunov A, Hansford JR, Ramaswamy V. Ultra high-risk PFA ependymoma is characterized by loss of chromosome 6q. Neuro Oncol 2021; 23:1360-1370. [PMID: 33580238 PMCID: PMC8328032 DOI: 10.1093/neuonc/noab034] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Within PF-EPN-A, 1q gain is a marker of poor prognosis, however, it is unclear if within PF-EPN-A additional cytogenetic events exist which can refine risk stratification. METHODS Five independent non-overlapping cohorts of PF-EPN-A were analyzed applying genome-wide methylation arrays for chromosomal and clinical variables predictive of survival. RESULTS Across all cohorts, 663 PF-EPN-A were identified. The most common broad copy number event was 1q gain (18.9%), followed by 6q loss (8.6%), 9p gain (6.5%), and 22q loss (6.8%). Within 1q gain tumors, there was significant enrichment for 6q loss (17.7%), 10q loss (16.9%), and 16q loss (15.3%). The 5-year progression-free survival (PFS) was strikingly worse in those patients with 6q loss, with a 5-year PFS of 50% (95% CI 45%-55%) for balanced tumors, compared with 32% (95% CI 24%-44%) for 1q gain only, 7.3% (95% CI 2.0%-27%) for 6q loss only and 0 for both 1q gain and 6q loss (P = 1.65 × 10-13). After accounting for treatment, 6q loss remained the most significant independent predictor of survival in PF-EPN-A but is not in PF-EPN-B. Distant relapses were more common in 1q gain irrespective of 6q loss. RNA sequencing comparing 6q loss to 6q balanced PF-EPN-A suggests that 6q loss forms a biologically distinct group. CONCLUSIONS We have identified an ultra high-risk PF-EPN-A ependymoma subgroup, which can be reliably ascertained using cytogenetic markers in routine clinical use. A change in treatment paradigm is urgently needed for this particular subset of PF-EPN-A where novel therapies should be prioritized for upfront therapy.
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Affiliation(s)
- Lorena V Baroni
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada.,Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lakshmikirupa Sundaresan
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ayala Heled
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hallie Coltin
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada.,Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Tong Lin
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Thomas E Merchant
- Department of Radiation Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Roger McLendon
- The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina, USA
| | - Claudia Faria
- Division of Neurosurgery, Centro Hospitalar Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Molly Buntine
- Hudson Institute of Medical Research, Clayton, Australia
| | | | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Terri S Armstrong
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Eric Bouffet
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sachin Kumar
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Neurosurgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kenneth D Aldape
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Nicholas G Gottardo
- Department of Paediatric Oncology and Haematology, Perth Children's Hospital, Perth, Australia
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Andrey Korshunov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jordan R Hansford
- Children's Cancer Centre, Royal Children's Hospital; Murdoch Children's Research Institute; Department of Pediatrics, University of Melbourne; Monash University, Melbourne, Australia
| | - Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, Ontario, Canada.,Programme in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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9
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Barthelson K, Pederson SM, Newman M, Lardelli M. Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer's disease. Mol Brain 2020; 13:142. [PMID: 33076949 PMCID: PMC7570131 DOI: 10.1186/s13041-020-00681-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/06/2020] [Indexed: 01/31/2023] Open
Abstract
To prevent or delay the onset of Alzheimer’s disease (AD), we must understand its molecular basis. The great majority of AD cases arise sporadically with a late onset after 65 years of age (LOAD). However, rare familial cases of AD can occur due to dominant mutations in a small number of genes that cause an early onset prior to 65 years of age (EOfAD). As EOfAD and LOAD share similar pathologies and disease progression, analysis of EOfAD genetic models may give insight into both subtypes of AD. Sortilin-related receptor 1 (SORL1) is genetically associated with both EOfAD and LOAD and provides a unique opportunity to investigate the relationships between both forms of AD. Currently, the role of SORL1 mutations in AD pathogenesis is unclear. To understand the molecular consequences of SORL1 mutation, we performed targeted mutagenesis of the orthologous gene in zebrafish. We generated an EOfAD-like mutation, V1482Afs, and a putatively null mutation, to investigate whether EOfAD-like mutations in sorl1 display haploinsufficiency by acting through loss-of-function mechanisms. We performed mRNA-sequencing on whole brains, comparing wild type fish with their siblings heterozygous for EOfAD-like or putatively loss-of-function mutations in sorl1, or transheterozygous for these mutations. Differential gene expression analysis identified a small number of differentially expressed genes due to the sorl1 genotypes. We also performed enrichment analysis on all detectable genes to obtain a more complete view on changes to gene expression by performing three methods of gene set enrichment analysis, then calculated an overall significance value using the harmonic mean p-value. This identified subtle effects on expression of genes involved in energy production, mRNA translation and mTORC1 signalling in both the EOfAD-like and null mutant brains, implying that these effects are due to sorl1 haploinsufficiency. Surprisingly, we also observed changes to expression of genes occurring only in the EOfAD-mutation carrier brains, suggesting gain-of-function effects. Transheterozygosity for the EOfAD-like and null mutations (i.e. lacking wild type sorl1), caused apparent effects on iron homeostasis and other transcriptome changes distinct from the single-mutation heterozygous fish. Our results provide insight into the possible early brain molecular effects of an EOfAD mutation in human SORL1. Differential effects of heterozygosity and complete loss of normal SORL1 expression are revealed.
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Affiliation(s)
- Karissa Barthelson
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.
| | - Stephen Martin Pederson
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, SA, 5005, Australia.
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10
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Yang X, Wu W, Pan Y, Zhou Q, Xu J, Han S. Immune-related genes in tumor-specific CD4 + and CD8 + T cells in colon cancer. BMC Cancer 2020; 20:585. [PMID: 32571262 PMCID: PMC7310260 DOI: 10.1186/s12885-020-07075-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022] Open
Abstract
Background Immune escape is an immunological mechanism underlying tumorigenesis, and T cells play an important role in this process. In this study, immune-related genes were evaluated in tumor-infiltrating CD4+ and CD8+ T cells in colon cancer. Methods ESTIMATE was used to calculate stromal and immune scores for tumor datasets downloaded from The Cancer Genome Atlas–Colon Cancer (COAD). Differentially expressed genes (DEGs) between samples with high and low stromal and immune scores were screened, followed by a functional enrichment analysis of the overlapping DEGs. The DEGs related to CD4+ and the CD8+ T cells were then screened. Predicted miRNA–mRNA and lncRNA–miRNA pairs were used to construct a competing endogenous RNA (ceRNA) network. Furthermore, chemical–gene interactions were predicted for genes in the ceRNA network. Kaplan–Meier survival curves were also plotted. Results In total, 83 stromal-related DEGs (5 up-regulated and 78 down-regulated) and 1270 immune-related DEGs (807 up-regulated and 293 down-regulated genes) were detected. The 79 overlapping DEGs were enriched for 39 biological process terms. Furthermore, 79 CD4+ T cell-related genes and 8 CD8+ T cell-related genes, such as ELK3, were screened. Additionally, ADAD1 and DLG3, related to CD4+ T cells, were significantly associated with the prognosis of patients with colon cancer. The chr22-38_28785274–29,006,793.1–miR-106a-5p-DDHD1 and chr22-38_28785274–29,006,793.1–miR-4319-GRHL1 axes obtained from CD4+ and CD8+ T cell-related ceRNAs were identified as candidates for further studies. Conclusion ELK3 is a candidate immune-related gene in colon cancer. The chr22-38_28785274–29,006,793.1–miR-106a-5p-DDHD1 and chr22-38_28785274–29,006,793.1–miR-4319-GRHL1 axes may be related to CD4+ and CD8+ T cell infiltration in colon cancer.
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Affiliation(s)
- Xi Yang
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops HuZhou University, No. 198 Hongqi Road, Huzhou, 313000, Zhejiang Province, China
| | - Wei Wu
- Department of Gastroenterology, Huzhou Cent Hosp, Affiliated Cent Hops HuZhou University, No.198 Hongqi Road, Huzhou, 313000, Zhejiang Province, China
| | - Yuefen Pan
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops HuZhou University, No. 198 Hongqi Road, Huzhou, 313000, Zhejiang Province, China
| | - Qing Zhou
- Department of Critical Care Medicine, Huzhou Cent Hosp, Affiliated Cent Hops HuZhou University, No. 198 Hongqi Road, Huzhou, 313000, Zhejiang Province, China
| | - Jiamin Xu
- Graduate School of Nursing, Huzhou University, No. 1 Bachelor Road, Huzhou, 313000, Zhejiang Province, China
| | - Shuwen Han
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops HuZhou University, No. 198 Hongqi Road, Huzhou, 313000, Zhejiang Province, China.
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11
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Saygin D, Tabib T, Bittar HET, Valenzi E, Sembrat J, Chan SY, Rojas M, Lafyatis R. Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertension. Pulm Circ 2020; 10:10.1177_2045894020908782. [PMID: 32166015 PMCID: PMC7052475 DOI: 10.1177/2045894020908782] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
Despite recent improvements in management of idiopathic pulmonary arterial
hypertension, mortality remains high. Understanding the alterations in the
transcriptome–phenotype of the key lung cells involved could provide insight
into the drivers of pathogenesis. In this study, we examined differential gene
expression of cell types implicated in idiopathic pulmonary arterial
hypertension from lung explants of patients with idiopathic pulmonary arterial
hypertension compared to control lungs. After tissue digestion, we analyzed all
cells from three idiopathic pulmonary arterial hypertension and six control
lungs using droplet-based single cell RNA-sequencing. After dimensional
reduction by t-stochastic neighbor embedding, we compared the transcriptomes of
endothelial cells, pericyte/smooth muscle cells, fibroblasts, and macrophage
clusters, examining differential gene expression and pathways implicated by
analysis of Gene Ontology Enrichment. We found that endothelial cells and
pericyte/smooth muscle cells had the most differentially expressed gene profile
compared to other cell types. Top differentially upregulated genes in
endothelial cells included novel genes: ROBO4, APCDD1, NDST1, MMRN2,
NOTCH4, and DOCK6, as well as previously reported
genes: ENG, ORAI2, TFDP1, KDR, AMOTL2, PDGFB, FGFR1, EDN1, and
NOTCH1. Several transcription factors were also found to be
upregulated in idiopathic pulmonary arterial hypertension endothelial cells
including SOX18, STRA13, LYL1, and ELK, which
have known roles in regulating endothelial cell phenotype. In particular,
SOX18 was implicated through bioinformatics analyses in
regulating the idiopathic pulmonary arterial hypertension endothelial cell
transcriptome. Furthermore, idiopathic pulmonary arterial hypertension
endothelial cells upregulated expression of FAM60A and
HDAC7, potentially affecting epigenetic changes in
idiopathic pulmonary arterial hypertension endothelial cells. Pericyte/smooth
muscle cells expressed genes implicated in regulation of cellular apoptosis and
extracellular matrix organization, and several ligands for genes showing
increased expression in endothelial cells. In conclusion, our study represents
the first detailed look at the transcriptomic landscape across idiopathic
pulmonary arterial hypertension lung cells and provides robust insight into
alterations that occur in vivo in idiopathic pulmonary arterial hypertension
lungs.
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Affiliation(s)
- Didem Saygin
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Humberto E T Bittar
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Eleanor Valenzi
- Division of Cardiology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Cardiology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Stephen Y Chan
- Division of Cardiology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Cardiology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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12
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Elia LP, Reisine T, Alijagic A, Finkbeiner S. Approaches to develop therapeutics to treat frontotemporal dementia. Neuropharmacology 2020; 166:107948. [PMID: 31962288 DOI: 10.1016/j.neuropharm.2020.107948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/16/2019] [Accepted: 01/07/2020] [Indexed: 12/13/2022]
Abstract
Frontotemporal degeneration (FTD) is a complex disease presenting as a spectrum of clinical disorders with progressive degeneration of frontal and temporal brain cortices and extensive neuroinflammation that result in personality and behavior changes, and eventually, death. There are currently no effective therapies for FTD. While 60-70% of FTD patients are sporadic cases, the other 30-40% are heritable (familial) cases linked to mutations in several known genes. We focus here on FTD caused by mutations in the GRN gene, which encodes a secreted protein, progranulin (PGRN), that has diverse roles in regulating cell survival, immune responses, and autophagy and lysosome function in the brain. FTD-linked mutations in GRN reduce brain PGRN levels that lead to autophagy and lysosome dysfunction, TDP43 accumulation, excessive microglial activation, astrogliosis, and neuron death through still poorly understood mechanisms. PGRN insufficiency has also been linked to Alzheimer's disease (AD), and so the development of therapeutics for GRN-linked FTD that restore PGRN levels and function may have broader application for other neurodegenerative diseases. This review focuses on a strategy to increase PGRN to functional, healthy levels in the brain by identifying novel genetic and chemical modulators of neuronal PGRN levels. This article is part of the special issue entitled 'The Quest for Disease-Modifying Therapies for Neurodegenerative Disorders'.
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Affiliation(s)
- Lisa P Elia
- Center for Systems and Therapeutics and Taube/Koret Center for Neurodegenerative Disease Research, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA.
| | - Terry Reisine
- Independent Scientific Consultant, Santa Cruz, CA, USA
| | - Amela Alijagic
- Center for Systems and Therapeutics and Taube/Koret Center for Neurodegenerative Disease Research, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics and Taube/Koret Center for Neurodegenerative Disease Research, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA; Departments of Neurology and Physiology, UCSF, San Francisco, CA, USA.
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13
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Wang S, Li J, Yang X. Long Non-Coding RNA LINC00525 Promotes the Stemness and Chemoresistance of Colorectal Cancer by Targeting miR-507/ELK3 Axis. Int J Stem Cells 2019; 12:347-359. [PMID: 31242722 PMCID: PMC6657946 DOI: 10.15283/ijsc19041] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Background and Objectives This study aims to explore the effects of a long non-coding RNA, LINC00525, on colorectal cancer (CRC) and its underlying molecular mechanisms. Methods The qPCR, MTT, colony formation, Western blotting, Luciferase reporter and biotin pull-down, shRNA knockdown and DNA fragmentation assays were performed in this study. Results High expressions of LINC00525 were associated with poor prognosis of CRC patients. LINC00525 knockdown decreased stemness properties and increased sensitivities to oxaliplatin. MiR-507 was a direct target of LINC00525 and overexpression of miR-507 significantly decreased abilities of tumorsphere formation and cell growth. Overexpression of miR-507 resulted in a decrease of expression of cancer stem cell markers and the increase of apoptosis rates. MiR-507 regulated the expression of ELK3. In addition, LINC00525 knockdown decreased the expression of ELK3. Restoration of ELK3 expression abrogated the effects of LINC00525 knockdown. LINC00525 could be served as prognostic marker of CRC. Conclusions LINC00525 enhanced stemness properties and increased sensitivities of CRC cells to oxaliplatin by targeting miR-507/ELK3 axis.
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Affiliation(s)
- Shunsheng Wang
- Department of Colorectal Surgery, Yidu Central Hospital of Weifang City, Qingzhou, China
| | - Jing Li
- Department of Colorectal Surgery, Yidu Central Hospital of Weifang City, Qingzhou, China
| | - Xiaopeng Yang
- Department of Colorectal Surgery, Yidu Central Hospital of Weifang City, Qingzhou, China
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14
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LRG1 Promotes Keratinocyte Migration and Wound Repair through Regulation of HIF-1α Stability. J Invest Dermatol 2019; 140:455-464.e8. [PMID: 31344385 DOI: 10.1016/j.jid.2019.06.143] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/13/2019] [Accepted: 06/30/2019] [Indexed: 01/10/2023]
Abstract
Re-epithelialization is a complex process during skin wound healing, and cell migration is an integral part of this phenomenon. Here we identified a role for LRG1 as a key regulator of epidermal keratinocyte migration where LRG1 acts via enhancement of HIF-1α stability. We showed that LRG1 is upregulated at murine skin wound edges and that addition of recombinant human LRG1 accelerates keratinocyte migration and skin wound healing. Furthermore, we identified transcription factor ELK3 as a downstream effector of LRG1. We confirmed that elevated ELK3 levels manipulated by LRG1 can promote cell migration through upregulation of HIF-1α stability. Because hyperglycemia complicatedly affects HIF-1α stability and activation, our findings provide insights into the molecular controls of wound-associated cell migration and identify potential therapeutic targets for the treatment of chronic diabetic wounds. In conclusion, we demonstrated that LRG1 promotes wound repair through keratinocyte migration and is important for normalization of an abnormal process of diabetic wound healing where HIF-1α stability is insufficient.
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15
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Griggio V, Vitale C, Todaro M, Riganti C, Kopecka J, Salvetti C, Bomben R, Bo MD, Magliulo D, Rossi D, Pozzato G, Bonello L, Marchetti M, Omedè P, Kodipad AA, Laurenti L, Del Poeta G, Mauro FR, Bernardi R, Zenz T, Gattei V, Gaidano G, Foà R, Massaia M, Boccadoro M, Coscia M. HIF-1α is over-expressed in leukemic cells from TP53-disrupted patients and is a promising therapeutic target in chronic lymphocytic leukemia. Haematologica 2019; 105:1042-1054. [PMID: 31289209 PMCID: PMC7109756 DOI: 10.3324/haematol.2019.217430] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022] Open
Abstract
In chronic lymphocytic leukemia (CLL), the hypoxia-inducible factor 1 (HIF-1) regulates the response of tumor cells to hypoxia and their protective interactions with the leukemic microenvironment. In this study, we demonstrate that CLL cells from TP53-disrupted (TP53dis) patients have constitutively higher expression levels of the α-subunit of HIF-1 (HIF-1α) and increased HIF-1 transcriptional activity compared to the wild-type counterpart. In the TP53dis subset, HIF-1α upregulation is due to reduced expression of the HIF-1α ubiquitin ligase von Hippel-Lindau protein (pVHL). Hypoxia and stromal cells further enhance HIF-1α accumulation, independently of TP53 status. Hypoxia acts through the downmodulation of pVHL and the activation of the PI3K/AKT and RAS/ERK1-2 pathways, whereas stromal cells induce an increased activity of the RAS/ERK1-2, RHOA/RHOA kinase and PI3K/AKT pathways, without affecting pVHL expression. Interestingly, we observed that higher levels of HIF-1A mRNA correlate with a lower susceptibility of leukemic cells to spontaneous apoptosis, and associate with the fludarabine resistance that mainly characterizes TP53dis tumor cells. The HIF-1α inhibitor BAY87-2243 exerts cytotoxic effects toward leukemic cells, regardless of the TP53 status, and has anti-tumor activity in Em-TCL1 mice. BAY87-2243 also overcomes the constitutive fludarabine resistance of TP53dis leukemic cells and elicits a strongly synergistic cytotoxic effect in combination with ibrutinib, thus providing preclinical evidence to stimulate further investigation into use as a potential new drug in CLL.
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Affiliation(s)
- Valentina Griggio
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Candida Vitale
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Maria Todaro
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, Turin, Italy
| | - Joanna Kopecka
- Department of Oncology, University of Turin, Turin, Italy
| | - Chiara Salvetti
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Riccardo Bomben
- Clinical and Experimental Onco-Hematology Unit, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Michele Dal Bo
- Clinical and Experimental Onco-Hematology Unit, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Daniela Magliulo
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Rossi
- Department of Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Gabriele Pozzato
- Department of Internal Medicine and Hematology, Maggiore General Hospital, University of Trieste, Trieste, Italy
| | - Lisa Bonello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Monia Marchetti
- Hematology Day Service, Oncology SOC, Hospital Cardinal Massaia, Asti, Italy
| | - Paola Omedè
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy
| | - Ahad Ahmed Kodipad
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Luca Laurenti
- Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Giovanni Del Poeta
- Division of Hematology, S. Eugenio Hospital and University of Tor Vergata, Rome, Italy
| | - Francesca Romana Mauro
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Policlinico Umberto I, Rome, Italy
| | - Rosa Bernardi
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Thorsten Zenz
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Valter Gattei
- Clinical and Experimental Onco-Hematology Unit, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Policlinico Umberto I, Rome, Italy
| | | | - Mario Boccadoro
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Marta Coscia
- Division of Hematology, A.O.U. Città della Salute e della Scienza di Torino, Turin, Italy .,Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
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16
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Elia LP, Mason AR, Alijagic A, Finkbeiner S. Genetic Regulation of Neuronal Progranulin Reveals a Critical Role for the Autophagy-Lysosome Pathway. J Neurosci 2019; 39:3332-3344. [PMID: 30696728 PMCID: PMC6788815 DOI: 10.1523/jneurosci.3498-17.2019] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 12/29/2022] Open
Abstract
Deficient progranulin levels cause dose-dependent neurological syndromes: haploinsufficiency leads to frontotemporal lobar degeneration (FTLD) and nullizygosity produces adult-onset neuronal ceroid lipofuscinosis. Mechanisms controlling progranulin levels are largely unknown. To better understand progranulin regulation, we performed a genome-wide RNAi screen using an ELISA-based platform to discover genes that regulate progranulin levels in neurons. We identified 830 genes that raise or lower progranulin levels by at least 1.5-fold in Neuro2a cells. When inhibited by siRNA or some by submicromolar concentrations of small-molecule inhibitors, 33 genes of the druggable genome increased progranulin levels in mouse primary cortical neurons; several of these also raised progranulin levels in FTLD model mouse neurons. "Hit" genes regulated progranulin by transcriptional or posttranscriptional mechanisms. Pathway analysis revealed enrichment of hit genes from the autophagy-lysosome pathway (ALP), suggesting a key role for this pathway in regulating progranulin levels. Progranulin itself regulates lysosome function. We found progranulin deficiency in neurons increased autophagy and caused abnormally enlarged lysosomes and boosting progranulin levels restored autophagy and lysosome size to control levels. Our data link the ALP to neuronal progranulin: progranulin levels are regulated by autophagy and, in turn, progranulin regulates the ALP. Restoring progranulin levels by targeting genetic modifiers reversed FTLD functional deficits, opening up potential opportunities for future therapeutics development.SIGNIFICANCE STATEMENT Progranulin regulates neuron and immune functions and is implicated in aging. Loss of one functional allele causes haploinsufficiency and leads to frontotemporal lobar degeneration (FTLD), the second leading cause of dementia. Progranulin gene polymorphisms are linked to Alzheimer's disease (AD) and complete loss of function causes neuronal ceroid lipofuscinosis. Despite the critical role of progranulin levels in neurodegenerative disease risk, almost nothing is known about their regulation. We performed an unbiased screen and identified specific pathways controlling progranulin levels in neurons. Modulation of these pathways restored levels in progranulin-deficient neurons and reversed FTLD phenotypes. We provide a new comprehensive understanding of the genetic regulation of progranulin levels and identify potential targets to treat FTLD and other neurodegenerative diseases, including AD.
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Affiliation(s)
- Lisa P Elia
- Center for Systems and Therapeutics and Taube/Koret Center for Neurodegenerative Disease Research, San Francisco, California,
- The J. David Gladstone Institutes, San Francisco, California 94158
| | - Amanda R Mason
- Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, and
| | - Amela Alijagic
- The J. David Gladstone Institutes, San Francisco, California 94158
| | - Steven Finkbeiner
- Center for Systems and Therapeutics and Taube/Koret Center for Neurodegenerative Disease Research, San Francisco, California,
- The J. David Gladstone Institutes, San Francisco, California 94158
- Departments of Neurology and Physiology, University of California, San Francisco, California 94143
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17
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RSK2-Mediated ELK3 Activation Enhances Cell Transformation and Breast Cancer Cell Growth by Regulation of c-fos Promoter Activity. Int J Mol Sci 2019; 20:ijms20081994. [PMID: 31018569 PMCID: PMC6515335 DOI: 10.3390/ijms20081994] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 12/14/2022] Open
Abstract
Ribosomal S6 kinase 2 (RSK2), regulated by Ras/Raf/MEKs/ERKs, transmits upstream activation signals to downstream substrates including kinases and transcription and epigenetic factors. We observed that ELK members, including ELK1, 3, and 4, highly interacted with RSK2. We further observed that the RSK2-ELK3 interaction was mediated by N-terminal kinase and linker domains of RSK2, and the D and C domains of ELK3, resulting in the phosphorylation of ELK3. Importantly, RSK2-mediated ELK3 enhanced c-fos promoter activity. Notably, chemical inhibition of RSK2 signaling using kaempferol (a RSK2 inhibitor) or U0126 (a selective MEK inhibitor) suppressed EGF-induced c-fos promoter activity. Moreover, functional deletion of RSK2 by knockdown or knockout showed that RSK2 deficiency suppressed EGF-induced c-fos promoter activity, resulting in inhibition of AP-1 transactivation activity and Ras-mediated foci formation in NIH3T3 cells. Immunocytofluorescence assay demonstrated that RSK2 deficiency reduced ELK3 localization in the nucleus. In MDA-MB-231 breast cancer cells, knockdown of RSK2 or ELK3 suppressed cell proliferation with accumulation at the G1 cell cycle phase, resulting in inhibition of foci formation and anchorage-independent cancer colony growth in soft agar. Taken together, these results indicate that a novel RSK2/ELK3 signaling axis, by enhancing c-Fos-mediated AP-1 transactivation activity, has an essential role in cancer cell proliferation and colony growth.
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Lee JH, Hur W, Hong SW, Kim JH, Kim SM, Lee EB, Yoon SK. ELK3 promotes the migration and invasion of liver cancer stem cells by targeting HIF-1α. Oncol Rep 2016; 37:813-822. [PMID: 27959451 DOI: 10.3892/or.2016.5293] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 06/25/2016] [Indexed: 11/06/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common solid cancer and the third most common cause of cancer-related mortality. HCC develops via a multistep process associated with genetic aberrations that facilitate HCC invasion and migration and promote metastasis. A growing body of evidence indicates that cancer stem cells (CSCs) are responsible for tumorigenesis, cancer cell invasion and metastasis. Despite the extremely small proportion of cancer cells represented by this subpopulation of HCC cells, CSCs play a key role in cancer metastasis and poor prognosis. ELK3 (Net/SAP-2/Erp) is a transcription factor that is activated by the Ras/extracellular signal-regulated kinase (ERK) signaling pathway. It plays several important roles in various physiological processes, including cell migration, invasion, wound healing, angiogenesis and tumorigenesis. In the present study, we investigated the role of ELK3 in cancer cell invasion and metastasis in CD133+/CD44+ liver cancer stem cells (LCSCs). We isolated LCSCs expressing CD133 and CD44 from Huh7 HCC cells and evaluated their metastatic potential using invasion and migration assays. We found that CD133+/CD44+ cells had increased metastatic potential compared with non-CD133+/CD44+ cells. We also demonstrated that ELK3 expression was upregulated in CD133+/CD44+ cells and that this aberration enhanced cell migration and invasion. In addition, we identified the molecular mechanism by which ELK3 promotes cancer cell migration and invasion. We found that silencing of ELK3 expression in CD133+/CD44+ LCSCs attenuated their metastatic potential by modulating the expression of heat shock-induced factor-1α (HIF-1α). Collectively, the results of the present study demonstrated that ELK3 overexpression promoted metastasis in CD133+/CD44+ cells by regulating HIF-1α expression and that silencing of ELK3 expression attenuated the metastatic potential of CD133+/CD44+ LCSCs. In conclusion, modulation of ELK3 expression may represent a novel therapeutic strategy for preventing HCC metastasis and invasion.
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Affiliation(s)
- Joon Ho Lee
- The Catholic University Liver Research Center and WHO Collaborating Center of Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Wonhee Hur
- The Catholic University Liver Research Center and WHO Collaborating Center of Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sung Woo Hong
- The Catholic University Liver Research Center and WHO Collaborating Center of Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Jung-Hee Kim
- The Catholic University Liver Research Center and WHO Collaborating Center of Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sung Min Kim
- The Catholic University Liver Research Center and WHO Collaborating Center of Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Eun Byul Lee
- The Catholic University Liver Research Center and WHO Collaborating Center of Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Seung Kew Yoon
- The Catholic University Liver Research Center and WHO Collaborating Center of Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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Cheng Q, Huang W, Chen N, Shang Y, Zhang H. SMC3 may play an important role in atopic asthma development. CLINICAL RESPIRATORY JOURNAL 2015; 10:469-76. [PMID: 25515564 DOI: 10.1111/crj.12247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 10/29/2014] [Accepted: 12/07/2014] [Indexed: 01/14/2023]
Abstract
INTRODUCTION As a common disease with a complex risk, including genetic and environmental factors, atopic asthma is prevalent but treatable. The aim of the study was to predict the underlying mechanism of asthma and identify target genes for the disease. METHODS The affymetrix chip data, GSE18965, were available from Gene Expression Omnibus and the differentially expressed genes (DEGs) between nine atopic asthmatic specimens and seven healthy nonatopic samples were identified by R. Then Gene Ontology and pathway enrichment analyses were performed to these DEGs. Further, search tool for the retrieval of interacting genes/proteins (STRING) was used to select protein-protein interaction (PPI) for DEGs, and then the network was visualized by Cytoscape. Finally, transcription factor binding site analysis was conducted to the hot gene. RESULTS Total 565 DEGs were identified, including 535 upregulated and 30 downregulated genes. The upregulated genes, such as structural maintenance of chromosome (SMC)3, significantly affected cellular component of extracellular matrix (P = 1.56E-04). Otherwise, DEGs were remarkably enriched in three pathways, including transforming growth factor-beta signaling pathway (P = 0.005252649). Further, SMC3 was detected as hot gene in PPI network, and NET (Elk3) was predicted as the significant transcription factor for this gene. CONCLUSION SMC3 may play an important role in atopic asthma development; therefore, it has the potential to be the target for the disease. Moreover, our findings provide more knowledge about the mechanism of atopic asthma and help the researchers to explore it in future.
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Affiliation(s)
- Qi Cheng
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wanjie Huang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ning Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yunxiao Shang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Han Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Robertson ED, Wasylyk C, Ye T, Jung AC, Wasylyk B. The oncogenic MicroRNA Hsa-miR-155-5p targets the transcription factor ELK3 and links it to the hypoxia response. PLoS One 2014; 9:e113050. [PMID: 25401928 PMCID: PMC4234625 DOI: 10.1371/journal.pone.0113050] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/18/2014] [Indexed: 12/29/2022] Open
Abstract
The molecular response to hypoxia is a critical cellular process implicated in cancer, and a target for drug development. The activity of the major player, HIF1α, is regulated at different levels by various factors, including the transcription factor ELK3. The molecular mechanisms of this intimate connection remain largely unknown. Whilst investigating global ELK3-chromatin interactions, we uncovered an unexpected connection that involves the microRNA hsa-miR-155-5p, a hypoxia-inducible oncomir that targets HIF1α. One of the ELK3 chromatin binding sites, detected by Chromatin Immuno-Precipitation Sequencing (ChIP-seq) of normal Human Umbilical Vein Endothelial Cells (HUVEC), is located at the transcription start site of the MIR155HG genes that expresses hsa-miR-155-5p. We confirmed that ELK3 binds to this promoter by ChIP and quantitative polymerase chain reaction (QPCR). We showed that ELK3 and hsa-miR-155-5p form a double-negative regulatory loop, in that ELK3 depletion induced hsa-miR-155-5p expression and hsa-miR-155-5p expression decreased ELK3 expression at the RNA level through a conserved target sequence in its 3'-UTR. We further showed that the activities of hsa-miR-155-5p and ELK3 are functionally linked. Pathway analysis indicates that both factors are implicated in related processes, including cancer and angiogenesis. Hsa-miR-155-5p expression and ELK3 depletion have similar effects on expression of known ELK3 target genes, and on in-vitro angiogenesis and wound closure. Bioinformatic analysis of cancer RNA-seq data shows that hsa-miR-155-5p and ELK3 expression are significantly anti-correlated, as would be expected from hsa-miR-155-5p targeting ELK3 RNA. Finally, hypoxia (0% oxygen) down-regulates ELK3 mRNA in a microRNA and hsa-miR-155-5p dependent manner. These results tie ELK3 into the hypoxia response pathway through an oncogenic microRNA and into a circuit implicated in the dynamics of the hypoxic response. This crosstalk could be important for the development of new treatments for a range of pathologies.
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Affiliation(s)
- E. Douglas Robertson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Christine Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Alain C. Jung
- Laboratoire de Biologie Tumorale, Centre Régional de Lutte Contre le Cancer Paul Strauss, EA3430 de l’Université de Strasbourg, Strasbourg, France
| | - Bohdan Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- * E-mail:
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Tsoyi K, Geldart AM, Christou H, Liu X, Chung SW, Perrella MA. Elk-3 is a KLF4-regulated gene that modulates the phagocytosis of bacteria by macrophages. J Leukoc Biol 2014; 97:171-80. [PMID: 25351511 DOI: 10.1189/jlb.4a0214-087r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
ETS family proteins play a role in immune responses. A unique member of this family, Elk-3, is a transcriptional repressor that regulates the expression of HO-1. Elk-3 is very sensitive to the effects of inflammatory mediators and is down-regulated by bacterial endotoxin (LPS). In the present study, exposure of mouse macrophages to Escherichia coli LPS resulted in decreased, full-length, and splice-variant isoforms of Elk-3. We isolated the Elk-3 promoter and demonstrated that LPS also decreased promoter activity. The Elk-3 promoter contains GC-rich regions that are putative binding sites for zinc-finger transcription factors, such as Sp1 and KLFs. Mutation of the GC-rich region from bp -613 to -603 blunted LPS-induced down-regulation of the Elk-3 promoter. Similar to the LPS response, coexpression of KLF4 led to repression of Elk-3 promoter activity, whereas coexpression of Sp1 increased activity. ChIP assays revealed that KLF4 binding to the Elk-3 promoter was increased by LPS exposure, and Sp1 binding was decreased. Thus, down-regulation of Elk-3 by bacterial LPS is regulated, in part, by the transcriptional repressor KLF4. Overexpression of Elk-3, in the presence of E. coli bacteria, resulted in decreased macrophage phagocytosis. To determine whether limited expression of HO-1 may contribute to this response, we exposed HO-1-deficient bone marrow-derived macrophages to E. coli and found a comparable reduction in bacterial phagocytosis. These data suggest that down-regulation of Elk-3 and the subsequent induction of HO-1 are important for macrophage function during the inflammatory response to infection.
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Affiliation(s)
- Konstantin Tsoyi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - Adriana M Geldart
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA; and
| | - Helen Christou
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA; and
| | - Xiaoli Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and Department of Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Su Wol Chung
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and School of Biological Sciences, University of Ulsan, South Korea
| | - Mark A Perrella
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and Department of Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
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22
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Thakur RK, Yadav VK, Kumar A, Singh A, Pal K, Hoeppner L, Saha D, Purohit G, Basundra R, Kar A, Halder R, Kumar P, Baral A, Kumar MJM, Baldi A, Vincenzi B, Lorenzon L, Banerjee R, Kumar P, Shridhar V, Mukhopadhyay D, Chowdhury S. Non-metastatic 2 (NME2)-mediated suppression of lung cancer metastasis involves transcriptional regulation of key cell adhesion factor vinculin. Nucleic Acids Res 2014; 42:11589-600. [PMID: 25249619 PMCID: PMC4191424 DOI: 10.1093/nar/gku860] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Tumor metastasis refers to spread of a tumor from site of its origin to distant organs and causes majority of cancer deaths. Although >30 metastasis suppressor genes (MSGs) that negatively regulate metastasis have been identified so far, two issues are poorly understood: first, which MSGs oppose metastasis in a tumor type, and second, which molecular function of MSG controls metastasis. Herein, integrative analyses of tumor-transcriptomes (n = 382), survival data (n = 530) and lymph node metastases (n = 100) in lung cancer patients identified non-metastatic 2 (NME2) as a key MSG from a pool of >30 metastasis suppressors. Subsequently, we generated a promoter-wide binding map for NME2 using chromatin immunoprecipitation with promoter microarrays (ChIP-chip), and transcriptome profiling. We discovered novel targets of NME2 which are involved in focal adhesion signaling. Importantly, we detected binding of NME2 in promoter of focal adhesion factor, vinculin. Reduced expression of NME2 led to enhanced transcription of vinculin. In comparison, NME1, a close homolog of NME2, did not bind to vinculin promoter nor regulate its expression. In line, enhanced metastasis of NME2-depleted lung cancer cells was found in zebrafish and nude mice tumor models. The metastatic potential of NME2-depleted cells was remarkably diminished upon selective RNA-i-mediated silencing of vinculin. Together, we demonstrate that reduced NME2 levels lead to transcriptional de-repression of vinculin and regulate lung cancer metastasis.
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Affiliation(s)
- Ram Krishna Thakur
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Vinod Kumar Yadav
- G.N.R. Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Akinchan Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Ankita Singh
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Krishnendu Pal
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Luke Hoeppner
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Dhurjhoti Saha
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Gunjan Purohit
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Richa Basundra
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Anirban Kar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Rashi Halder
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Pankaj Kumar
- G.N.R. Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Aradhita Baral
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - M J Mahesh Kumar
- Animal House, Centre For Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Alfonso Baldi
- Department of Biochemistry, Section of Pathology, Second University of Naples, Italy
| | | | - Laura Lorenzon
- Department of Surgery, University La Sapienza, Rome, Italy
| | - Rajkumar Banerjee
- Division of Lipid Science and Technology, Indian Institute of Chemical Technology, Hyderabad, India
| | - Praveen Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
| | - Viji Shridhar
- Department of Experimental Pathology, Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Shantanu Chowdhury
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India G.N.R. Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
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Heo SH, Cho JY. ELK3 suppresses angiogenesis by inhibiting the transcriptional activity of ETS-1 on MT1-MMP. Int J Biol Sci 2014; 10:438-47. [PMID: 24719561 PMCID: PMC3979996 DOI: 10.7150/ijbs.8095] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 03/07/2014] [Indexed: 11/05/2022] Open
Abstract
Ets transcription factors play important roles in vasculogenesis and angiogenesis. Knockout of the Ets gene family members in mice resulted in disrupted angiogenesis and malformed vascular systems. In this study, the role and mechanism of ELK3, an Ets factor, in angiogenesis was investigated using ELK3-specific siRNA in human vascular endothelial cells (HUVECs) and in vivo implantation assay. The suppression of ELK3 expression resulted in the reinforcement of VEGF-induced tube formation in HUVECs. The in vivo Matrigel plug assay also showed that ELK3 knockdown resulted in increased angiogenesis. Luciferase activity of the MT1-MMP promoter induced by ETS-1 factor was attenuated ELK3 co-transfection. CHIP assay showed the binding of ELK3 on the MT1-MMP promoter. MT1-MMP knockdown in the ELK3 knockdowned cells resulted in the decrease of tube formation suggesting that MT1-MMP transcriptional repression is required for ELK3-mediated anti-angiogenesis effect. Our data also showed that the suppressive effect of ELK3 on the angiogenesis was partly due to the inhibitory effect of ELK3 to the ETS-1 transcriptional activity on the MT1-MMP promoter rather than direct suppression of ELK3 on the target gene, since the expression level of co-repressor Sin3A is low in endothelial cells. Our results suggest that ELK3 plays a negative role of VEGF-induced angiogenesis through indirectly inhibiting ETS-1 function.
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Affiliation(s)
- Sun-Hee Heo
- Department of Veterinary Biochemistry, BK21 Plus, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Veterinary Biochemistry, BK21 Plus, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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Robertson ED, Semenchenko K, Wasylyk B. Crosstalk between Mdm2, p53 and HIF1-α: distinct responses to oxygen stress and implications for tumour hypoxia. Subcell Biochem 2014; 85:199-214. [PMID: 25201196 DOI: 10.1007/978-94-017-9211-0_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The E3 ubiquitin ligase Mdm2 regulates two transcription factors, p53 and HIF1α, which appear to be tailored towards different and specific roles within the cell, the DNA damage and hypoxia responses, respectively. However, evidence increasingly points towards the interplay between these factors being crucial for the regulation of cellular metabolism and survival in times of oxygen stress, which has particular relevance for tumour formation. Mdm2, p53 and HIF1α all respond to hypoxia, and intriguingly, have distinct roles depending on the level of hypoxia. The data from numerous studies across different conditions hint at the interplay between these key factors in cellular homeostasis. Here we try to weave these strands together, to create a picture of the complex tapestry of interactions that demonstrates the importance of the crosstalk between these key regulatory proteins during hypoxia.
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Affiliation(s)
- E Douglas Robertson
- Department of Functional Genomics and Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMC, UMR 7104 CNRS-UdS, U946 INSERM, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
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25
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Weinl C, Riehle H, Park D, Stritt C, Beck S, Huber G, Wolburg H, Olson EN, Seeliger MW, Adams RH, Nordheim A. Endothelial SRF/MRTF ablation causes vascular disease phenotypes in murine retinae. J Clin Invest 2013; 123:2193-206. [PMID: 23563308 DOI: 10.1172/jci64201] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 02/07/2013] [Indexed: 11/17/2022] Open
Abstract
Retinal vessel homeostasis ensures normal ocular functions. Consequently, retinal hypovascularization and neovascularization, causing a lack and an excess of vessels, respectively, are hallmarks of human retinal pathology. We provide evidence that EC-specific genetic ablation of either the transcription factor SRF or its cofactors MRTF-A and MRTF-B, but not the SRF cofactors ELK1 or ELK4, cause retinal hypovascularization in the postnatal mouse eye. Inducible, EC-specific deficiency of SRF or MRTF-A/MRTF-B during postnatal angiogenesis impaired endothelial tip cell filopodia protrusion, resulting in incomplete formation of the retinal primary vascular plexus, absence of the deep plexi, and persistence of hyaloid vessels. All of these features are typical of human hypovascularization-related vitreoretinopathies, such as familial exudative vitreoretinopathies including Norrie disease. In contrast, conditional EC deletion of Srf in adult murine vessels elicited intraretinal neovascularization that was reminiscent of the age-related human pathologies retinal angiomatous proliferation and macular telangiectasia. These results indicate that angiogenic homeostasis is ensured by differential stage-specific functions of SRF target gene products in the developing versus the mature retinal vasculature and suggest that the actin-directed MRTF-SRF signaling axis could serve as a therapeutic target in the treatment of human vascular retinal diseases.
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Affiliation(s)
- Christine Weinl
- Department for Molecular Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
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Li B, Wan X, Zhu Q, Li L, Zeng Y, Hu D, Qian Y, Lu L, Wang X, Meng X. Net expression inhibits the growth of pancreatic ductal adenocarcinoma cell PL45 in vitro and in vivo. PLoS One 2013; 8:e57818. [PMID: 23469073 PMCID: PMC3585156 DOI: 10.1371/journal.pone.0057818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/26/2013] [Indexed: 11/25/2022] Open
Abstract
Pancreatic ductal adenocarcinoma has a poor prognosis due to late diagnosis and a lack of effective therapeutic options. Thus, it is important to better understand its molecular mechanisms and to develop more effective treatments for the disease. The ternary complex factor Net, which exerts its strong inhibitory function on transcription of proto-oncogene gene c-fos by forming ternary complexes with a second transcription factor, has been suspected of being involved in pancreatic cancer and other tumors biology. In this study, we found that the majority of pancreatic ductal adenocarcinoma tissues and cell lines had weak or no expression of Net, whereas significantly high level of Net expression occurred in paired adjacent normal tissues we studied. Furthermore, using in vitro and in vivo model systems, we found that overexpression of Net inhibited cell growth and survival and induced cell apoptosis in human pancreatic ductal adenocarcinoma cell PL45; the mechanisms by which Net inhibited the cell cycle progression were mainly through P21-Cyclin D1/CDK4 Pathway. Our data thus suggested that Net might play an important role in pancreatic carcinogenesis, possibly by acting as a tumor suppressor gene.
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Affiliation(s)
- Baiwen Li
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xinjian Wan
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qi Zhu
- Department of Gastroenterology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Lei Li
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yue Zeng
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Duanmin Hu
- Department of Gastroenterology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yueqin Qian
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Lungen Lu
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xingpeng Wang
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- * E-mail: (XW); (XM)
| | - Xiangjun Meng
- Department of Gastroenterology, Shanghai First People’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- * E-mail: (XW); (XM)
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Wong CSF, Sceneay J, House CM, Halse HM, Liu MCP, George J, Hunnam TCUP, Parker BS, Haviv I, Ronai Z, Cullinane C, Bowtell DD, Möller A. Vascular normalization by loss of Siah2 results in increased chemotherapeutic efficacy. Cancer Res 2012; 72:1694-704. [PMID: 22354750 DOI: 10.1158/0008-5472.can-11-3310] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tumor hypoxia is associated with resistance to antiangiogenic therapy and poor prognosis. The Siah E3 ubiquitin ligases regulate the hypoxic response pathway by modulating the turnover of the master proangiogenic transcription factor hypoxia-inducible factor-1α (Hif-1α). In this study, we show that genetic deficiency in the Siah family member Siah2 results in vascular normalization and delayed tumor growth in an established transgenic model of aggressive breast cancer. Tumors arising in a Siah2(-/-) genetic background showed increased perfusion and pericyte-associated vasculature, similar to that occurring with antiangiogenic therapy. In support of the role of Siah2 in regulating levels of Hif-1α, expression of angiogenic factors was decreased in Siah2(-/-) tumors. Blood vessel normalization in Siah2(-/-) tumors resulted in an increased response to chemotherapy and prolonged survival. Together, our findings offer a preclinical proof of concept that targeting Siah2 is sufficient to attenuate Hif-1α-mediated angiogenesis and hypoxia signaling, thereby improving responses to chemotherapy.
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Affiliation(s)
- Christina S F Wong
- Cancer Genomics and Genetics, Peter MacCallum Cancer Centre, St Andrew's Place, East Melbourne, Victoria, Australia
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28
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Serchov T, Dubois-Pot-Schneider H, Charlot C, Rösl F, Wasylyk B. Involvement of net and Hif1alpha in distinct yet intricately linked hypoxia-induced signaling pathways. J Biol Chem 2010; 285:21223-32. [PMID: 20427288 DOI: 10.1074/jbc.m110.121723] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The present study compares negative Ets transcription factor (Net) and hypoxia-inducible factor 1alpha (HIF1alpha) regulation by hypoxia. Their protein stabilities are differently regulated by hypoxia, defining three periods in the kinetics: normoxia (high Net levels and low HIF1alpha levels), early hypoxia (high levels of Net and HIF1alpha), and late hypoxia (degradation of Net and HIF1alpha). Modulators of prolyl hydroxylase domain protein (PHD) activity induce a mobility shift of Net, similar to HIF1alpha, suggesting that post-translational modifications of both factors depend on PHD activity. The three PHDs have different roles in the regulation of Net protein levels; PHD1 and PHD3 are involved in the stabilization of Net, whereas PHD2 controls its degradation in late hypoxia. Net physically interacts with PHD2 in hypoxia, whereas PHD1 and PHD3 bind to Net in normoxia and hypoxia. Under the same conditions, PHD2 and PHD3 regulate both HIF1alpha stabilization in early hypoxia and its degradation at late hypoxia, whereas PHD1 is involved in HIF1alpha degradation in late hypoxia. We describe interconnections between the regulation of both Net and HIF1alpha at the protein level. Evidence is provided for a direct physical interaction between Net and HIF1alpha and indirect transcriptional regulation loops that involve the PHDs. Taken together our results indicate that Net and HIF1alpha are components of distinct signaling pathways that are intricately linked.
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Affiliation(s)
- Tsvetan Serchov
- Unité Mixte de Recherche 7104 Centre National de la Recherche Scientifique, Université de Strasbourg-U, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, Graffenstaden, France
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29
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Charlot C, Dubois-Pot H, Serchov T, Tourrette Y, Wasylyk B. A review of post-translational modifications and subcellular localization of Ets transcription factors: possible connection with cancer and involvement in the hypoxic response. Methods Mol Biol 2010; 647:3-30. [PMID: 20694658 DOI: 10.1007/978-1-60761-738-9_1] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Post-translational modifications and subcellular localizations modulate transcription factors, generating a code that is deciphered into an activity. We describe our current understanding of these processes for Ets factors, which have recently been recognized for their importance in various biological processes. We present the global picture for the family, and then focus on particular aspects related to cancer and hypoxia. The analysis of Post-translational modification and cellular localization is only beginning to enter the age of "omic," high content, systems biology. Our snap-shots of particularly active fields point to the directions in which new techniques will be needed, in our search for a more complete description of regulatory pathways.
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Affiliation(s)
- Céline Charlot
- Department of Cancer Biology, Institute de Genetique et de Biologie, Moleculaire et Cellulaire, Lille, France
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30
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Fasanaro P, Greco S, Lorenzi M, Pescatori M, Brioschi M, Kulshreshtha R, Banfi C, Stubbs A, Calin GA, Ivan M, Capogrossi MC, Martelli F. An integrated approach for experimental target identification of hypoxia-induced miR-210. J Biol Chem 2009; 284:35134-43. [PMID: 19826008 PMCID: PMC2787374 DOI: 10.1074/jbc.m109.052779] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 10/02/2009] [Indexed: 12/11/2022] Open
Abstract
miR-210 is a key player of cell response to hypoxia, modulating cell survival, VEGF-driven endothelial cell migration, and the ability of endothelial cells to form capillary-like structures. A crucial step in understanding microRNA (miRNA) function is the identification of their targets. However, only few miR-210 targets have been identified to date. Here, we describe an integrated strategy for large-scale identification of new miR-210 targets by combining transcriptomics and proteomics with bioinformatic approaches. To experimentally validate candidate targets, the RNA-induced silencing complex (RISC) loaded with miR-210 was purified by immunoprecipitation along with its mRNA targets. The complex was significantly enriched in mRNAs of 31 candidate targets, such as BDNF, GPD1L, ISCU, NCAM, and the non-coding RNA Xist. A subset of the newly identified targets was further confirmed by 3'-untranslated region (UTR) reporter assays, and hypoxia induced down-modulation of their expression was rescued blocking miR-210, providing support for the approach validity. In the case of 9 targets, such as PTPN1 and P4HB, miR-210 seed-pairing sequences localized in the coding sequence or in the 5'-UTR, in line with recent data extending miRNA targeting beyond the "classic" 3'-UTR recognition. Finally, Gene Ontology analysis of the targets highlights known miR-210 impact on cell cycle regulation and differentiation, and predicts a new role of this miRNA in RNA processing, DNA binding, development, membrane trafficking, and amino acid catabolism. Given the complexity of miRNA actions, we view such a multiprong approach as useful to adequately describe the multiple pathways regulated by miR-210 during physiopathological processes.
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Affiliation(s)
- Pasquale Fasanaro
- From the IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Simona Greco
- From the IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy
| | - Maria Lorenzi
- the Istituto Nazionale di Riposo e Cura per Anziani, 60121 Ancona, Italy
| | | | - Maura Brioschi
- the Centro Cardiologico Monzino-IRCCS, 20138 Milan, Italy
| | | | - Cristina Banfi
- the Centro Cardiologico Monzino-IRCCS, 20138 Milan, Italy
| | - Andrew Stubbs
- the Erasmus Medical Centre, 3015 Rotterdam, The Netherlands
| | | | - Mircea Ivan
- Indiana University, Indianapolis, Indiana 46202, and
| | | | - Fabio Martelli
- the Istituto Dermopatico dell'Immacolata-IRCCS, 00167 Rome, Italy
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31
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Abstract
The ras/Raf/Mek/Erk pathway plays a central role in coordinating endothelial cell activities during angiogenesis. Transcription factors Ets1 and Ets2 are targets of ras/Erk signaling pathways that have been implicated in endothelial cell function in vitro, but their precise role in vascular formation and function in vivo remains ill-defined. In this work, mutation of both Ets1 and Ets2 resulted in embryonic lethality at midgestation, with striking defects in vascular branching having been observed. The action of these factors was endothelial cell autonomous as demonstrated using Cre/loxP technology. Analysis of Ets1/Ets2 target genes in isolated embryonic endothelial cells demonstrated down-regulation of Mmp9, Bcl-X(L), and cIAP2 in double mutants versus controls, and chromatin immunoprecipitation revealed that both Ets1 and Ets2 were loaded at target promoters. Consistent with these observations, endothelial cell apoptosis was significantly increased both in vivo and in vitro when both Ets1 and Ets2 were mutated. These results establish essential and overlapping functions for Ets1 and Ets2 in coordinating endothelial cell functions with survival during embryonic angiogenesis.
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32
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Hong SW, Yoo JW, Kang HS, Kim S, Lee DK. HIF-1alpha-dependent gene expression program during the nucleic acid-triggered antiviral innate immune responses. Mol Cells 2009; 27:243-50. [PMID: 19277508 DOI: 10.1007/s10059-009-0030-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 12/04/2008] [Accepted: 12/06/2008] [Indexed: 01/28/2023] Open
Abstract
Recent studies suggest a novel role of HIF-1alpha under non-hypoxic conditions, including antibacterial and antiviral innate immune responses. However, the identity of the pathogen-associated molecular pattern which triggers HIF-1alpha activation during the antiviral response remains to be identified. Here, we demonstrate that cellular administration of double-stranded nucleic acids, the molecular mimics of viral genomes, results in the induction of HIF-1alpha protein level as well as the increase in HIF-1alpha target gene expression. Whole-genome DNA microarray analysis revealed that double-stranded nucleic acid treatment triggers induction of a number of hypoxia-inducible genes, and induction of these genes are compromised upon siRNA-mediated HIF-1alpha knock-down. Interestingly, HIF-1alpha knock-down also resulted in down-regulation of a number of genes involved in antiviral innate immune responses. Our study demonstrates that HIF-1alpha activation upon nucleic acid-triggered antiviral innate immune responses plays an important role in regulation of genes involved in not only hypoxic response, but also immune response.
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Affiliation(s)
- Sun Woo Hong
- Department of Chemistry and Brain Korea 21 School of Chemical Materials Science, Sungkyunkwan University, Suwon, 440-746, Korea
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