51
|
Díaz-Bulnes P, Saiz ML, López-Larrea C, Rodríguez RM. Crosstalk Between Hypoxia and ER Stress Response: A Key Regulator of Macrophage Polarization. Front Immunol 2020; 10:2951. [PMID: 31998288 PMCID: PMC6961549 DOI: 10.3389/fimmu.2019.02951] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022] Open
Abstract
Macrophage activation and polarization are closely linked with metabolic rewiring, which is required to sustain their biological functions. These metabolic alterations allow the macrophages to adapt to the microenvironment changes associated with inflammation or tissue damage (hypoxia, nutrient imbalance, oxidative stress, etc.) and to fulfill their highly energy-demanding proinflammatory and anti-microbial functions. This response is integrated via metabolic sensors that coordinate these metabolic fluxes with their functional requirements. Here we review how the metabolic and phenotypic plasticity of macrophages are intrinsically connected with the hypoxia stress sensors and the unfolded protein response in the endoplasmic reticulum, and how these molecular pathways participate in the maladaptive polarization of macrophages in human pathology and chronic inflammation.
Collapse
Affiliation(s)
- Paula Díaz-Bulnes
- Translational Immunology Laboratory, Health Research Institute of the Principality of Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - María Laura Saiz
- Translational Immunology Laboratory, Health Research Institute of the Principality of Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carlos López-Larrea
- Translational Immunology Laboratory, Health Research Institute of the Principality of Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain.,Immunology Service, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ramón M Rodríguez
- Translational Immunology Laboratory, Health Research Institute of the Principality of Asturias, Hospital Universitario Central de Asturias, Oviedo, Spain
| |
Collapse
|
52
|
Doynova M, Chatzieleftheriadis K, Roderick HL. Mitochondrial Ca 2+ laMety directs fibrosis. Cell Calcium 2019; 86:102155. [PMID: 31911235 DOI: 10.1016/j.ceca.2019.102155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022]
Abstract
During development, disease or in response to changes in local environmental and/or nutrient supply, cellular metabolism is substantially remodeled. Reduced mitochondrial Ca2+ uptake was recently reported to induce metabolic remodeling, which through stimulating alterations in the epigenome causes changes in gene expression associated with fibroblast to myofibroblast differentiation.
Collapse
Affiliation(s)
- Malina Doynova
- KU Leuven, Department of Cardiovascular Sciences, Laboratory of Experimental Cardiology, 3000 Leuven, Belgium
| | | | - H Llewelyn Roderick
- KU Leuven, Department of Cardiovascular Sciences, Laboratory of Experimental Cardiology, 3000 Leuven, Belgium; K.G. Jebsen Center for Cardiac Research, University of Oslo, Oslo, Norway.
| |
Collapse
|
53
|
Dandawate P, Ghosh C, Palaniyandi K, Paul S, Rawal S, Pradhan R, Sayed AAA, Choudhury S, Standing D, Subramaniam D, Padhye S, Gunewardena S, Thomas SM, O’ Neil M, Tawfik O, Welch DR, Jensen RA, Maliski S, Weir S, Iwakuma T, Anant S, Dhar A. The Histone Demethylase KDM3A, Increased in Human Pancreatic Tumors, Regulates Expression of DCLK1 and Promotes Tumorigenesis in Mice. Gastroenterology 2019; 157:1646-1659.e11. [PMID: 31442435 PMCID: PMC6878178 DOI: 10.1053/j.gastro.2019.08.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/31/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS The histone lysine demethylase 3A (KDM3A) demethylates H3K9me1 and H3K9Me2 to increase gene transcription and is upregulated in tumors, including pancreatic tumors. We investigated its activities in pancreatic cancer cell lines and its regulation of the gene encoding doublecortin calmodulin-like kinase 1 (DCLK1), a marker of cancer stem cells. METHODS We knocked down KDM3A in MiaPaCa-2 and S2-007 pancreatic cancer cell lines and overexpressed KDM3A in HPNE cells (human noncancerous pancreatic ductal cell line); we evaluated cell migration, invasion, and spheroid formation under hypoxic and normoxic conditions. Nude mice were given orthotopic injections of S2-007 cells, with or without (control) knockdown of KDM3A, and HPNE cells, with or without (control) overexpression of KDM3A; tumor growth was assessed. We analyzed pancreatic tumor tissues from mice and pancreatic cancer cell lines by immunohistochemistry and immunoblotting. We performed RNA-sequencing analysis of MiaPaCa-2 and S2-007 cells with knockdown of KDM3A and evaluated localization of DCLK1 and KDM3A by immunofluorescence. We analyzed the cancer genome atlas for levels of KDM3A and DCLK1 messenger RNA in human pancreatic ductal adenocarcinoma (PDAC) tissues and association with patient survival time. RESULTS Levels of KDM3A were increased in human pancreatic tumor tissues and cell lines, compared with adjacent nontumor pancreatic tissues, such as islet and acinar cells. Knockdown of KDM3A in S2-007 cells significantly reduced colony formation, invasion, migration, and spheroid formation, compared with control cells, and slowed growth of orthotopic tumors in mice. We identified KDM3A-binding sites in the DCLK1 promoter; S2-007 cells with knockdown of KDM3A had reduced levels of DCLK1. HPNE cells that overexpressed KDM3A formed foci and spheres in culture and formed tumors and metastases in mice, whereas control HPNE cells did not. Hypoxia induced sphere formation and increased levels of KDM3A in S2-007 cells and in HPNE cells that overexpressed DCLK1, but not control HPNE cells. Levels of KDM3A and DCLK1 messenger RNA were higher in human PDAC than nontumor pancreatic tissues and correlated with shorter survival times of patients. CONCLUSIONS We found human PDAC samples and pancreatic cancer cell lines to overexpress KDM3A. KDM3A increases expression of DCLK1, and levels of both proteins are increased in human PDAC samples. Knockdown of KDM3A in pancreatic cancer cell lines reduced their invasive and sphere-forming activities in culture and formation of orthotopic tumors in mice. Hypoxia increased expression of KDM3A in pancreatic cancer cells. Strategies to disrupt this pathway might be developed for treatment of pancreatic cancer.
Collapse
Affiliation(s)
- Prasad Dandawate
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Chandrayee Ghosh
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Kanagaraj Palaniyandi
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Santanu Paul
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Sonia Rawal
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Rohan Pradhan
- Interdisciplinary Science and Technology Research Academy, Abeda Inamdar Senior College, Camp, Pune 411001, India
| | - Afreen Asif Ali Sayed
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Sonali Choudhury
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - David Standing
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Dharmalingam Subramaniam
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Subhash Padhye
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA.,Interdisciplinary Science and Technology Research Academy, Abeda Inamdar Senior College, Camp, Pune 411001, India
| | - Sumedha Gunewardena
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Sufi M. Thomas
- Department of Otolaryngology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Moura O’ Neil
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Ossama Tawfik
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Danny R. Welch
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Roy A. Jensen
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Sally Maliski
- School of Nursing, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Scott Weir
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Tomoo Iwakuma
- Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Shrikant Anant
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.
| | - Animesh Dhar
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.
| |
Collapse
|
54
|
The Critical Role of Hypoxic Microenvironment and Epigenetic Deregulation in Esophageal Cancer Radioresistance. Genes (Basel) 2019; 10:genes10110927. [PMID: 31739546 PMCID: PMC6896142 DOI: 10.3390/genes10110927] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/01/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
Esophageal cancer (EC) is the seventh most common cancer worldwide and the sixth leading cause of death, according to Globocan 2018. Despite efforts made for therapeutic advances, EC remains highly lethal, portending a five-year overall survival of just 15-20%. Hence, the discovery of new molecular targets that might improve therapeutic efficacy is urgently needed. Due to high proliferative rates and also the limited oxygen and nutrient diffusion in tumors, the development of hypoxic regions and consequent activation of hypoxia-inducible factors (HIFs) are a common characteristic of solid tumors, including EC. Accordingly, HIF-1α, involved in cell cycle deregulation, apoptosis, angiogenesis induction and proliferation in cancer, constitutes a predictive marker of resistance to radiotherapy (RT). Deregulation of epigenetic mechanisms, including aberrant DNA methylation and histone modifications, have emerged as critical factors in cancer development and progression. Recently, interactions between epigenetic enzymes and HIF-1α transcription factors have been reported. Thus, further insight into hypoxia-induced epigenetic alterations in EC may allow the identification of novel therapeutic targets and predictive biomarkers, impacting on patient survival and quality of life.
Collapse
|
55
|
Lal S, Comer JM, Konduri PC, Shah A, Wang T, Lewis A, Shoffner G, Guo F, Zhang L. Heme promotes transcriptional and demethylase activities of Gis1, a member of the histone demethylase JMJD2/KDM4 family. Nucleic Acids Res 2019; 46:215-228. [PMID: 29126261 PMCID: PMC5758875 DOI: 10.1093/nar/gkx1051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
The yeast Gis1 protein is a transcriptional regulator belonging to the JMJD2/KDM4 subfamily of demethylases that contain a JmjC domain, which are highly conserved from yeast to humans. They have important functions in histone methylation, cellular signaling and tumorigenesis. Besides serving as a cofactor in many proteins, heme is known to directly regulate the activities of proteins ranging from transcriptional regulators to potassium channels. Here, we report a novel mechanism governing heme regulation of Gis1 transcriptional and histone demethylase activities. We found that two Gis1 modules, the JmjN + JmjC domain and the zinc finger (ZnF), can bind to heme specifically in vitro. In vivo functional analysis showed that the ZnF, not the JmjN + JmjC domain, promotes heme activation of transcriptional activity. Likewise, measurements of the demethylase activity of purified Gis1 proteins showed that full-length Gis1 and the JmjN + JmjC domain both possess demethylase activity. However, heme potentiates the demethylase activity of full-length Gis1, but not that of the JmjN + JmjC domain, which can confer heme activation of transcriptional activity in an unrelated protein. These results demonstrate that Gis1 represents a novel class of multi-functional heme sensing and signaling proteins, and that heme binding to the ZnF stimulates Gis1 demethylase and transcriptional activities.
Collapse
Affiliation(s)
- Sneha Lal
- Department of Biological Sciences, University of Texas at Dallas, Mail Stop RL11, 800 W. Campbell Road, Richardson, TX 75080, USA
| | - Jonathan M Comer
- Department of Biological Sciences, University of Texas at Dallas, Mail Stop RL11, 800 W. Campbell Road, Richardson, TX 75080, USA
| | - Purna C Konduri
- Department of Biological Sciences, University of Texas at Dallas, Mail Stop RL11, 800 W. Campbell Road, Richardson, TX 75080, USA
| | - Ajit Shah
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Tianyuan Wang
- Department of Biological Sciences, University of Texas at Dallas, Mail Stop RL11, 800 W. Campbell Road, Richardson, TX 75080, USA
| | - Anthony Lewis
- Department of Biological Sciences, University of Texas at Dallas, Mail Stop RL11, 800 W. Campbell Road, Richardson, TX 75080, USA
| | - Grant Shoffner
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Li Zhang
- Department of Biological Sciences, University of Texas at Dallas, Mail Stop RL11, 800 W. Campbell Road, Richardson, TX 75080, USA
| |
Collapse
|
56
|
Kharrati-Koopaee H, Ebrahimie E, Dadpasand M, Niazi A, Esmailizadeh A. Genomic analysis reveals variant association with high altitude adaptation in native chickens. Sci Rep 2019; 9:9224. [PMID: 31239472 PMCID: PMC6592930 DOI: 10.1038/s41598-019-45661-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 03/12/2019] [Indexed: 01/10/2023] Open
Abstract
Native chickens are endangered genetic resources that are kept by farmers for different purposes. Native chickens distributed in a wide range of altitudes, have developed adaptive mechanisms to deal with hypoxia. For the first time, we report variants associated with high-altitude adaptation in Iranian native chickens by whole genome sequencing of lowland and highland chickens. We found that these adaptive variants are involved in DNA repair, organs development, immune response and histone binding. Amazingly, signature selection analysis demonstrated that differential variants are adaptive in response to hypoxia and are not due to other evolutionary pressures. Cellular component analysis of variants showed that mitochondrion is the most important organelle for hypoxia adaptation. A total of 50 variants was detected in mtDNA for highland and lowland chickens. High-altitude associated with variant discovery highlighted the importance of COX3, a gene involved in cell respiration, in hypoxia adaptation. The results of study suggest that MIR6644-2 is involved in hypoxia and high-altitude adaptations by regulation of embryo development. Finally, 3877 novel SNVs including the mtDNA ones, were submitted to EBI (PRJEB24944). Whole-genome sequencing and variant discovery of native chickens provided novel insights about adaptation mechanisms and highlights the importance of valuable genomic variants in chickens.
Collapse
Affiliation(s)
| | - Esmaeil Ebrahimie
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran.
- The University of Adelaide, School of Animal and Veterinary Sciences, Adelaide, South Australia, Australia.
- School of Information Technology and Mathematical Science, Division of Information Technology, Engineering and the Environment, University of South Australia, South Australia, Adelaide, Australia.
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia.
| | - Mohammad Dadpasand
- Department of Animal science, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Esmailizadeh
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, P.R. China.
- Department of Animal science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.
| |
Collapse
|
57
|
Miedel MT, Gavlock DC, Jia S, Gough A, Taylor DL, Stern AM. Modeling the Effect of the Metastatic Microenvironment on Phenotypes Conferred by Estrogen Receptor Mutations Using a Human Liver Microphysiological System. Sci Rep 2019; 9:8341. [PMID: 31171849 PMCID: PMC6554298 DOI: 10.1038/s41598-019-44756-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/23/2019] [Indexed: 02/08/2023] Open
Abstract
Reciprocal coevolution of tumors and their microenvironments underlies disease progression, yet intrinsic limitations of patient-derived xenografts and simpler cell-based models present challenges towards a deeper understanding of these intercellular communication networks. To help overcome these barriers and complement existing models, we have developed a human microphysiological system (MPS) model of the human liver acinus, a common metastatic site, and have applied this system to estrogen receptor (ER)+ breast cancer. In addition to their hallmark constitutive (but ER-dependent) growth phenotype, different ESR1 missense mutations, prominently observed during estrogen deprivation therapy, confer distinct estrogen-enhanced growth and drug resistant phenotypes not evident under cell autonomous conditions. Under low molecular oxygen within the physiological range (~5–20%) of the normal liver acinus, the estrogen-enhanced growth phenotypes are lost, a dependency not observed in monoculture. In contrast, the constitutive growth phenotypes are invariant within this range of molecular oxygen suggesting that ESR1 mutations confer a growth advantage not only during estrogen deprivation but also at lower oxygen levels. We discuss the prospects and limitations of implementing human MPS, especially in conjunction with in situ single cell hyperplexed computational pathology platforms, to identify biomarkers mechanistically linked to disease progression that inform optimal therapeutic strategies for patients.
Collapse
Affiliation(s)
- Mark T Miedel
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dillon C Gavlock
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shanhang Jia
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA.,School of Medicine, Tsinghua University, Beijing, China
| | - Albert Gough
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - D Lansing Taylor
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA. .,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA. .,University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
| | - Andrew M Stern
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA. .,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
58
|
Chen YL, Zhang Y, Wang J, Chen N, Fang W, Zhong J, Liu Y, Qin R, Yu X, Sun Z, Gao F. A 17 gene panel for non-small-cell lung cancer prognosis identified through integrative epigenomic-transcriptomic analyses of hypoxia-induced epithelial-mesenchymal transition. Mol Oncol 2019; 13:1490-1502. [PMID: 30973670 PMCID: PMC6599842 DOI: 10.1002/1878-0261.12491] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 03/01/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
As a critical feature of the tumor microenvironment, hypoxia is known to be a potent inducer of tumor metastasis, and it has been proposed that the initial steps in metastasis involve epithelial–mesenchymal transition (EMT). The strong correlation among hypoxia, EMT, and metastasis suggests that integrative assessment of gene expression and the DNA modification program of hypoxia‐induced EMT via high‐throughput sequencing technologies may increase our understanding of the molecular basis of tumor invasion and metastasis. Here, we present the genomewide transcriptional and epigenetic profiles of non‐small‐cell lung cancer (NSCLC) cells under normoxic and hypoxic conditions. We demonstrate that hypoxia induces EMT along with dynamic alterations of transcriptional expression and epigenetic modifications in both A549 and HCC827 cells. After training using a dataset from patients with invasive and noninvasive lung adenocarcinomas with an artificial neural network algorithm, a characteristic 17‐gene panel was identified, consisting of genes involved in EMT, hypoxia response, glycometabolism, and epigenetic modifications. This 17‐gene signature clearly stratified NSCLC patients with significant differences in overall survival across three independent datasets. Our study may be suitable as a basis for further selection of gene signatures to potentially guide prognostic stratification in patients with NSCLC.
Collapse
Affiliation(s)
- Yue-Lei Chen
- Stem Cell Bank/Stem Cell Core Facility, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yihe Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Na Chen
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Weiying Fang
- Stem Cell Bank/Stem Cell Core Facility, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianing Zhong
- Institute of Genomic Medicine, Wenzhou Medical University, China
| | - Yi Liu
- Stem Cell Bank/Stem Cell Core Facility, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rui Qin
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinxin Yu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, China.,Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, China
| | - Fei Gao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Institute of Genomic Medicine, Wenzhou Medical University, China
| |
Collapse
|
59
|
Abstract
Hypoxia signals directly to chromatin via histone demethylases to alter gene expression
Collapse
Affiliation(s)
- Paolo Gallipoli
- Wellcome Trust-MRC Cambridge Stem Cell Institute; Department of Haematology, University of Cambridge; and Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute; Department of Haematology, University of Cambridge; and Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK.
| |
Collapse
|
60
|
Chakraborty AA, Laukka T, Myllykoski M, Ringel AE, Booker MA, Tolstorukov MY, Meng YJ, Meier SR, Jennings RB, Creech AL, Herbert ZT, McBrayer SK, Olenchock BA, Jaffe JD, Haigis MC, Beroukhim R, Signoretti S, Koivunen P, Kaelin WG. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science 2019; 363:1217-1222. [PMID: 30872525 DOI: 10.1126/science.aaw1026] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
Abstract
Oxygen sensing is central to metazoan biology and has implications for human disease. Mammalian cells express multiple oxygen-dependent enzymes called 2-oxoglutarate (OG)-dependent dioxygenases (2-OGDDs), but they vary in their oxygen affinities and hence their ability to sense oxygen. The 2-OGDD histone demethylases control histone methylation. Hypoxia increases histone methylation, but whether this reflects direct effects on histone demethylases or indirect effects caused by the hypoxic induction of the HIF (hypoxia-inducible factor) transcription factor or the 2-OG antagonist 2-hydroxyglutarate (2-HG) is unclear. Here, we report that hypoxia promotes histone methylation in a HIF- and 2-HG-independent manner. We found that the H3K27 histone demethylase KDM6A/UTX, but not its paralog KDM6B, is oxygen sensitive. KDM6A loss, like hypoxia, prevented H3K27 demethylation and blocked cellular differentiation. Restoring H3K27 methylation homeostasis in hypoxic cells reversed these effects. Thus, oxygen directly affects chromatin regulators to control cell fate.
Collapse
Affiliation(s)
- Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Tuomas Laukka
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, FIN-90014 Oulu, Finland
| | - Matti Myllykoski
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, FIN-90014 Oulu, Finland
| | - Alison E Ringel
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew A Booker
- Department of Informatics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Michael Y Tolstorukov
- Department of Informatics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Yuzhong Jeff Meng
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,The Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel R Meier
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Rebecca B Jennings
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda L Creech
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zachary T Herbert
- Molecular Biology Core Facility, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Samuel K McBrayer
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Benjamin A Olenchock
- Division of Cardiovascular Medicine, Department of Medicine, The Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, FIN-90014 Oulu, Finland.
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
61
|
Wilson C, Krieg AJ. KDM4B: A Nail for Every Hammer? Genes (Basel) 2019; 10:E134. [PMID: 30759871 PMCID: PMC6410163 DOI: 10.3390/genes10020134] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
Epigenetic changes are well-established contributors to cancer progression and normal developmental processes. The reversible modification of histones plays a central role in regulating the nuclear processes of gene transcription, DNA replication, and DNA repair. The KDM4 family of Jumonj domain histone demethylases specifically target di- and tri-methylated lysine 9 on histone H3 (H3K9me3), removing a modification central to defining heterochromatin and gene repression. KDM4 enzymes are generally over-expressed in cancers, making them compelling targets for study and therapeutic inhibition. One of these family members, KDM4B, is especially interesting due to its regulation by multiple cellular stimuli, including DNA damage, steroid hormones, and hypoxia. In this review, we discuss what is known about the regulation of KDM4B in response to the cellular environment, and how this context-dependent expression may be translated into specific biological consequences in cancer and reproductive biology.
Collapse
Affiliation(s)
- Cailin Wilson
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA.
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
| |
Collapse
|
62
|
Lamadema N, Burr S, Brewer AC. Dynamic regulation of epigenetic demethylation by oxygen availability and cellular redox. Free Radic Biol Med 2019; 131:282-298. [PMID: 30572012 DOI: 10.1016/j.freeradbiomed.2018.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023]
Abstract
The chromatin structure of the mammalian genome must facilitate both precisely-controlled DNA replication together with tightly-regulated gene transcription. This necessarily involves complex mechanisms and processes which remain poorly understood. It has long been recognised that the epigenetic landscape becomes established during embryonic development and acts to specify and determine cell fate. In addition, the chromatin structure is highly dynamic and allows for both cellular reprogramming and homeostatic modulation of cell function. In this respect, the functions of epigenetic "erasers", which act to remove covalently-linked epigenetic modifications from DNA and histones are critical. The enzymatic activities of the TET and JmjC protein families have been identified as demethylases which act to remove methyl groups from DNA and histones, respectively. Further, they are characterised as members of the Fe(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. This provides the intriguing possibility that their enzymatic activities may be modulated by cellular metabolism, oxygen availability and redox-based mechanisms, all of which are likely to display dynamic cell- and tissue-specific patterns of flux. Here we discuss the current evidence for such [O2]- and redox-dependent regulation of the TET and Jmjc demethylases and the potential physiological and pathophysiological functional consequences of such regulation.
Collapse
Affiliation(s)
- Nermina Lamadema
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Simon Burr
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Alison C Brewer
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom.
| |
Collapse
|
63
|
Al Tameemi W, Dale TP, Al-Jumaily RMK, Forsyth NR. Hypoxia-Modified Cancer Cell Metabolism. Front Cell Dev Biol 2019; 7:4. [PMID: 30761299 PMCID: PMC6362613 DOI: 10.3389/fcell.2019.00004] [Citation(s) in RCA: 301] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022] Open
Abstract
While oxygen is critical to the continued existence of complex organisms, extreme levels of oxygen within a system, known as hypoxia (low levels of oxygen) and hyperoxia (excessive levels of oxygen), potentially promote stress within a defined biological environment. The consequences of tissue hypoxia, a result of a defective oxygen supply, vary in response to the gravity, extent and environment of the malfunction. Persistent pathological hypoxia is incompatible with normal biological functions, and as a result, multicellular organisms have been compelled to develop both organism-wide and cellular-level hypoxia solutions. Both direct, including oxidative phosphorylation down-regulation and inhibition of fatty-acid desaturation, and indirect processes, including altered hypoxia-sensitive transcription factor expression, facilitate the metabolic modifications that occur in response to hypoxia. Due to the dysfunctional vasculature associated with large areas of some cancers, sections of these tumors continue to develop in hypoxic environments. Crucial to drug development, a robust understanding of the significance of these metabolism changes will facilitate our understanding of cancer cell survival. This review defines our current knowledge base of several of the hypoxia-instigated modifications in cancer cell metabolism and exemplifies the correlation between metabolic change and its support of the hypoxic-adapted malignancy.
Collapse
Affiliation(s)
- Wafaa Al Tameemi
- Faculty of Medicine and Health Sciences, Institute for Science and Technology in Medicine, Keele University, Staffordshire, United Kingdom
| | - Tina P. Dale
- Faculty of Medicine and Health Sciences, Institute for Science and Technology in Medicine, Keele University, Staffordshire, United Kingdom
| | - Rakad M. Kh Al-Jumaily
- Faculty of Medicine and Health Sciences, Institute for Science and Technology in Medicine, Keele University, Staffordshire, United Kingdom
- Department of Biology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Nicholas R. Forsyth
- Faculty of Medicine and Health Sciences, Institute for Science and Technology in Medicine, Keele University, Staffordshire, United Kingdom
| |
Collapse
|
64
|
Walport LJ, Schofield CJ. Adventures in Defining Roles of Oxygenases in the Regulation of Protein Biosynthesis. CHEM REC 2018; 18:1760-1781. [PMID: 30151867 DOI: 10.1002/tcr.201800056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The 2-oxoglutarate (2OG) dependent oxygenases were first identified as having roles in the post-translational modification of procollagen in animals. Subsequently in plants and microbes, they were shown to have roles in the biosynthesis of many secondary metabolites, including signalling molecules and the penicillin/cephalosporin antibiotics. Crystallographic studies of microbial 2OG oxygenases and related enzymes, coupled to DNA sequence analyses, led to the prediction that 2OG oxygenases are widely distributed in aerobic biology. This personal account begins with examples of the roles of 2OG oxygenases in antibiotic biosynthesis, and then describes efforts to assign functions to other predicted 2OG oxygenases. In humans, 2OG oxygenases have been found to have roles in small molecule metabolism, as well as in the epigenetic regulation of protein and nucleic acid biosynthesis and function. The roles and functions of human 2OG oxygenases are compared, focussing on discussion of their substrate and product selectivities. The account aims to emphasize how scoping the substrate selectivity of, sometimes promiscuous, enzymes can provide insights into their functions and so enable therapeutic work.
Collapse
Affiliation(s)
- Louise J Walport
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
65
|
Liu G, Shegiwal A, Zeng Y, Wei Y, Boyer C, Haddleton D, Tao L. Polymers for Fluorescence Imaging of Formaldehyde in Living Systems via the Hantzsch Reaction. ACS Macro Lett 2018; 7:1346-1352. [PMID: 35651241 DOI: 10.1021/acsmacrolett.8b00697] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Formaldehyde (FA) has been detected via the Hantzsch reaction for many decades. However, the Hantzsch reaction has been rarely used to detect FA in biological systems due to the disadvantages of small-molecule probes (including toxicity and poor water solubility). In this study, polymeric fluorescent probes were developed to resolve these issues associated with small molecules, and FA in living systems was successfully detected via the Hantzsch reaction. These water-soluble polymers were easily scaled-up (∼25 g) by radical polymerization using commercial monomers. These polymers exhibited similar, albeit better, sensitivity to FA compared to water-soluble small molecules, primarily indicative of the advantages of polymers for the detection of FA via the Hantzsch reaction. The polymer structures were highly biocompatible with the probes; thus, these polymers can effectively detect endogenous FA in cells or zebrafish in a safe manner. This result confirmed the superiority of polymers in safety as biocompatible materials. This study highlights a straightforward method for exploring probes for the detection of FA in living systems. It offers functional polymers for bioimaging and extends the application scope of the Hantzsch reaction, reflecting the utility of a broad study of organic reactions in interdisciplinary fields as well as possible key implications in organic chemistry, analytical chemistry, and polymer chemistry.
Collapse
Affiliation(s)
- Guoqiang Liu
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN), School of Chemical Engineering, UNSW Australia, Sydney, NSW 2052, Australia
| | - Ataulla Shegiwal
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U. K
| | - Yuan Zeng
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yen Wei
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Cyrille Boyer
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN), School of Chemical Engineering, UNSW Australia, Sydney, NSW 2052, Australia
| | - David Haddleton
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U. K
| | - Lei Tao
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| |
Collapse
|
66
|
Biamonti G, Maita L, Montecucco A. The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell Metabolism. Front Oncol 2018; 8:408. [PMID: 30319972 PMCID: PMC6168629 DOI: 10.3389/fonc.2018.00408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a pervasive mechanism that molds the transcriptome to meet cell and organism needs. However, how this layer of gene expression regulation is coordinated with other aspects of the cell metabolism is still largely undefined. Glucose is the main energy and carbon source of the cell. Not surprisingly, its metabolism is finely tuned to satisfy growth requirements and in response to nutrient availability. A number of studies have begun to unveil the connections between glucose metabolism and splicing programs. Alternative splicing modulates the ratio between M1 and M2 isoforms of pyruvate kinase in this way determining the choice between aerobic glycolysis and complete glucose oxidation in the Krebs cycle. Reciprocally, intermediates in the Krebs cycle may impact splicing programs at different levels by modulating the activity of 2-oxoglutarate-dependent oxidases. In this review we discuss the molecular mechanisms that coordinate alternative splicing programs with glucose metabolism, two aspects with profound implications in human diseases.
Collapse
Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Lucia Maita
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | | |
Collapse
|
67
|
Mahalingam SM, Chu H, Liu X, Leamon CP, Low PS. Carbonic Anhydrase IX-Targeted Near-Infrared Dye for Fluorescence Imaging of Hypoxic Tumors. Bioconjug Chem 2018; 29:3320-3331. [PMID: 30185025 DOI: 10.1021/acs.bioconjchem.8b00509] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Use of tumor-targeted fluorescence dyes to help surgeons identify otherwise undetected tumor nodules, decrease the incidence of cancer-positive margins, and facilitate localization of malignant lymph nodes has demonstrated considerable promise for improving cancer debulking surgery. Unfortunately, the repertoire of available tumor-targeted fluorescent dyes does not permit identification of all cancer types, raising the need to develop additional tumor-specific fluorescent dyes to ensure localization of all malignant lesions during cancer surgeries. By comparing the mRNA levels of the hypoxia-induced plasma membrane protein carbonic anhydrase IX (CA IX) in 13 major human cancers with the same mRNA levels in corresponding normal tissues, we document that CA IX constitutes a nearly universal marker for the design of tumor-targeted fluorescent dyes. Motivated by this expression profile, we synthesize two new CA IX-targeted near-infrared (NIR) fluorescent imaging agents and characterize their physical and biological properties both in vitro and in vivo. We report that conjugation of either acetazolamide or 6-aminosaccharin (i.e., two CA-IX-specific ligands) to the NIR fluorescent dye, S0456, via an extended phenolic spacer creates a brightly fluorescent dye that binds CA IX with high affinity and allows rapid visualization of hypoxic regions of solid tumors at depths >1 cm beneath a tissue surface. Taken together, these data suggest that a CA IX-targeted NIR dye can constitute a useful addition to a cocktail of tumor-targeted NIR dyes designed to image all human cancers.
Collapse
Affiliation(s)
| | - Haiyan Chu
- Endocyte Inc. , 3000 Kent Avenue , West Lafayette , Indiana 47906 , United States
| | | | - Christopher P Leamon
- Endocyte Inc. , 3000 Kent Avenue , West Lafayette , Indiana 47906 , United States
| | | |
Collapse
|
68
|
Araos J, Sleeman JP, Garvalov BK. The role of hypoxic signalling in metastasis: towards translating knowledge of basic biology into novel anti-tumour strategies. Clin Exp Metastasis 2018; 35:563-599. [DOI: 10.1007/s10585-018-9930-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/13/2018] [Indexed: 02/06/2023]
|
69
|
Hu CJ, Zhang H, Laux A, Pullamsetti SS, Stenmark KR. Mechanisms contributing to persistently activated cell phenotypes in pulmonary hypertension. J Physiol 2018; 597:1103-1119. [PMID: 29920674 PMCID: PMC6375873 DOI: 10.1113/jp275857] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/16/2018] [Indexed: 12/24/2022] Open
Abstract
Chronic pulmonary hypertension (PH) is characterized by the accumulation of persistently activated cell types in the pulmonary vessel exhibiting aberrant expression of genes involved in apoptosis resistance, proliferation, inflammation and extracellular matrix (ECM) remodelling. Current therapies for PH, focusing on vasodilatation, do not normalize these activated phenotypes. Furthermore, current approaches to define additional therapeutic targets have focused on determining the initiating signals and their downstream effectors that are important in PH onset and development. Although these approaches have produced a large number of compelling PH treatment targets, many promising human drugs have failed in PH clinical trials. Herein, we propose that one contributing factor to these failures is that processes important in PH development may not be good treatment targets in the established phase of chronic PH. We hypothesize that this is due to alterations of chromatin structure in PH cells, resulting in functional differences between the same factor or pathway in normal or early PH cells versus cells in chronic PH. We propose that the high expression of genes involved in the persistently activated phenotype of PH vascular cells is perpetuated by an open chromatin structure and multiple transcription factors (TFs) via the recruitment of high levels of epigenetic regulators including the histone acetylases P300/CBP, histone acetylation readers including BRDs, the Mediator complex and the positive transcription elongation factor (Abstract figure). Thus, determining how gene expression is controlled by examining chromatin structure, TFs and epigenetic regulators associated with aberrantly expressed genes in pulmonary vascular cells in chronic PH, may uncover new PH therapeutic targets.
![]()
Collapse
Affiliation(s)
- Cheng-Jun Hu
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hui Zhang
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aya Laux
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Soni S Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, member of the German Center for Lung Research (DZL), Bad Nauheim, Germany.,Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), member of the DZL, Justus-Liebig University, Giessen, Germany
| | - Kurt R Stenmark
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
70
|
Targeting cancer stem cells and their niche: perspectives for future therapeutic targets and strategies. Semin Cancer Biol 2018; 53:139-155. [PMID: 30081228 DOI: 10.1016/j.semcancer.2018.08.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/30/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023]
Abstract
A small subpopulation of cells within the bulk of tumors share features with somatic stem cells, in that, they are capable of self-renewal, they differentiate, and are highly resistant to conventional therapy. These cells have been referred to as cancer stem cells (CSCs). Recent reports support the central importance of a cancer stem cell-like niche that appears to help foster the generation and maintenance of CSCs. In response to signals provided by this microenvironment, CSCs express the tumorigenic characteristics that can drive tumor metastasis by the induction of epithelial-mesenchymal-transition (EMT) that in turn fosters the migration and recolonization of the cells as secondary tumors within metastatic niches. We summarize here recent advances in cancer stem cell research including the characterization of their genetic and epigenetic features, metabolic specialities, and crosstalk with aging-associated processes. Potential strategies for targeting CSCs, and their niche, by regulating CSCs plasticity, or therapeutic sensitivity is discussed. Finally, it is hoped that new strategies and related therapeutic approaches as outlined here may help prevent the formation of the metastatic niche, as well as counter tumor progression and metastatic growth.
Collapse
|
71
|
Ascorbic acid induces global epigenetic reprogramming to promote meiotic maturation and developmental competence of porcine oocytes. Sci Rep 2018; 8:6132. [PMID: 29666467 PMCID: PMC5904140 DOI: 10.1038/s41598-018-24395-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/03/2018] [Indexed: 01/01/2023] Open
Abstract
L-ascorbic acid (Vitamin C) can enhance the meiotic maturation and developmental competence of porcine oocytes, but the underlying molecular mechanism remains obscure. Here we show the role of ascorbic acid in regulating epigenetic status of both nucleic acids and chromatin to promote oocyte maturation and development in pigs. Supplementation of 250 μM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (AA2P) during in vitro maturation significantly enhanced the nuclear maturation (as indicated by higher rate of first polar body extrusion and increased Bmp15 mRNA level), reduced level of reactive oxygen species, and promoted developmental potency (higher cleavage and blastocyst rates of parthenotes, and decreased Bax and Caspase3 mRNA levels in blastocysts) of pig oocytes. AA2P treatment caused methylation erasure in mature oocytes on nucleic acids (5-methylcytosine (5 mC) and N 6 -methyladenosine (m6A)) and histones (Histone H3 trimethylations at lysines 27, H3K27me3), but establishment of histone H3 trimethylations at lysines 4 (H3K4me3) and 36 (H3K36me3). During the global methylation reprogramming process, levels of TET2 (mRNA and protein) and Dnmt3b (mRNA) were significantly elevated, but simultaneously DNMT3A (mRNA and protein), and also Hif-1α, Hif-2α, Tet3, Mettl14, Kdm5b and Eed (mRNA) were significantly inhibited. Our findings support that ascorbic acid can reprogram the methylation status of not only DNA and histone, but also RNA, to improve pig oocyte maturation and developmental competence.
Collapse
|
72
|
Kitajima S, Lee KL, Fujioka M, Sun W, You J, Chia GS, Wanibuchi H, Tomita S, Araki M, Kato H, Poellinger L. Hypoxia-inducible factor-2 alpha up-regulates CD70 under hypoxia and enhances anchorage-independent growth and aggressiveness in cancer cells. Oncotarget 2018; 9:19123-19135. [PMID: 29721188 PMCID: PMC5922382 DOI: 10.18632/oncotarget.24919] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
Hypoxia-inducible factors (HIFs) facilitate cellular adaptation to environmental stress such as low oxygen conditions (hypoxia) and consequently promote tumor growth. While HIF-1α functions in cancer progression have been increasingly recognized, the contribution of HIF-2α remains widely unclear despite accumulating reports showing its overexpression in cancer cells. Here, we report that HIF-2α up-regulates the expression of CD70, a cancer-related surface antigen that improves anchorage-independent growth in cancer cells and is associated with poor clinical prognosis, which can be induced via epigenetic modifications mediated by DNMT1. The ablation of CD70 by RNAi led to decreased colony forming efficiency in soft agar. Most strikingly, we identified the emergence of CD70-expressing cells derived from CD70-negative cell lines upon prolonged hypoxia exposure or DNMT1 inhibition, both of which significantly reduced CpG-nucleotide methylations within CD70 promoter region. Interestingly, DNMT1 expression was decreased under hypoxia, which was rescued by HIF-2α knockdown. In addition, the expression of CD70 and colony forming efficiency in soft agar were decreased by knockdown of HIF-2α. These findings indicate that CD70 expression and an aggressive phenotype of cancer cells is driven under hypoxic conditions and mediated by HIF-2α functions and epigenetic modifications. This provides additional insights into the role of HIF-2α in coordinated regulation of stem-like functions and epigenetics that are important for cancer progression and may present additional targets for the development of novel combinatorial therapeutics.
Collapse
Affiliation(s)
- Shojiro Kitajima
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Pharmacology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Kian Leong Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Masaki Fujioka
- Department of Molecular Pathology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Wendi Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jia You
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Grace Sushin Chia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Hideki Wanibuchi
- Department of Molecular Pathology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Shuhei Tomita
- Department of Pharmacology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Marito Araki
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hiroyuki Kato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Lorenz Poellinger
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
73
|
Bargiela D, Burr SP, Chinnery PF. Mitochondria and Hypoxia: Metabolic Crosstalk in Cell-Fate Decisions. Trends Endocrinol Metab 2018; 29:249-259. [PMID: 29501229 DOI: 10.1016/j.tem.2018.02.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 01/07/2023]
Abstract
Alterations in mitochondrial metabolism influence cell differentiation and growth. This process is regulated by the activity of 2-oxoglutarate (2OG)-dependent dioxygenases (2OGDDs) - a diverse superfamily of oxygen-consuming enzymes - through modulation of the epigenetic landscape and transcriptional responses. Recent reports have described the role of mitochondrial metabolites in directing 2OGDD-driven cell-fate switches in stem cells (SCs), immune cells, and cancer cells. An understanding of the metabolic mechanisms underlying 2OGDD autoregulation is required for therapeutic targeting of this system. We propose a model dependent on oxygen and metabolite availability and discuss how this integrates 2OGDD metabolic signalling, the hypoxic transcriptional response, and fate-determining epigenetic changes.
Collapse
Affiliation(s)
- David Bargiela
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stephen P Burr
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.
| |
Collapse
|
74
|
Burr S, Caldwell A, Chong M, Beretta M, Metcalf S, Hancock M, Arno M, Balu S, Kropf VL, Mistry RK, Shah AM, Mann GE, Brewer AC. Oxygen gradients can determine epigenetic asymmetry and cellular differentiation via differential regulation of Tet activity in embryonic stem cells. Nucleic Acids Res 2018; 46:1210-1226. [PMID: 29186571 PMCID: PMC5814828 DOI: 10.1093/nar/gkx1197] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 02/06/2023] Open
Abstract
Graded levels of molecular oxygen (O2) exist within developing mammalian embryos and can differentially regulate cellular specification pathways. During differentiation, cells acquire distinct epigenetic landscapes, which determine their function, however the mechanisms which regulate this are poorly understood. The demethylation of 5-methylcytosine (5mC) is achieved via successive oxidation reactions catalysed by the Ten-Eleven-Translocation (Tet) enzymes, yielding the 5-hydroxymethylcytosine (5hmC) intermediate. These require O2 as a co-factor, and hence may link epigenetic processes directly to O2 gradients during development. We demonstrate that the activities of Tet enzymes display distinct patterns of [O2]-dependency, and that Tet1 activity, specifically, is subject to differential regulation within a range of O2 which is physiologically relevant in embryogenesis. Further, differentiating embryonic stem cells displayed a transient burst of 5hmC, which was both dependent upon Tet1 and inhibited by low (1%) [O2]. A GC-rich promoter region within the Tet3 locus was identified as a significant target of this 5mC-hydroxylation. Further, this region was shown to associate with Tet1, and display the histone epigenetic marks, H3K4me3 and H3K27me3, which are characteristic of a bivalent, developmentally 'poised' promoter. We conclude that Tet1 activity, determined by [O2] may play a critical role in regulating cellular differentiation and fate in embryogenesis.
Collapse
Affiliation(s)
- Simon Burr
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Anna Caldwell
- King's Centre of Excellence for Mass Spectrometry, King's College London, London SE1 9NH, UK
| | - Mei Chong
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Matteo Beretta
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Stephen Metcalf
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Matthew Hancock
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Matthew Arno
- King's Genomic Centre, King's College London, London SE1 9NH, UK
| | - Sucharitha Balu
- King's Genomic Centre, King's College London, London SE1 9NH, UK
| | - Valeria Leon Kropf
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Rajesh K Mistry
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Ajay M Shah
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Giovanni E Mann
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| | - Alison C Brewer
- British Heart Foundation Centre of Research Excellence, Department of Cardiology, King's College London, London SE5 9NU, UK
| |
Collapse
|
75
|
Assenov Y, Brocks D, Gerhäuser C. Intratumor heterogeneity in epigenetic patterns. Semin Cancer Biol 2018; 51:12-21. [PMID: 29366906 DOI: 10.1016/j.semcancer.2018.01.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/24/2017] [Accepted: 01/17/2018] [Indexed: 02/08/2023]
Abstract
Analogous to life on earth, tumor cells evolve through space and time and adapt to different micro-environmental conditions. As a result, tumors are composed of millions of genetically diversified cells at the time of diagnosis. Profiling these variants contributes to understanding tumors' clonal origins and might help to better understand response to therapy. However, even genetically homogenous cell populations show remarkable diversity in their response to different environmental stimuli, suggesting that genetic heterogeneity does not explain the full spectrum of tumor plasticity. Understanding epigenetic diversity across cancer cells provides important additional information about the functional state of subclones and therefore allows better understanding of tumor evolution and resistance to current therapies.
Collapse
Affiliation(s)
- Yassen Assenov
- Epigenomics and Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - David Brocks
- Epigenomics and Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Clarissa Gerhäuser
- Epigenomics and Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| |
Collapse
|
76
|
Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
Collapse
|
77
|
Lee S, Lee J, Chae S, Moon Y, Lee HY, Park B, Yang EG, Hwang D, Park H. Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. Nucleic Acids Res 2017; 45:11643-11657. [PMID: 28977425 PMCID: PMC5714201 DOI: 10.1093/nar/gkx747] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023] Open
Abstract
Hypoxia increases both active and repressive histone methylation levels via decreased activity of histone demethylases. However, how such increases coordinately regulate induction or repression of hypoxia-responsive genes is largely unknown. Here, we profiled active and repressive histone tri-methylations (H3K4me3, H3K9me3, and H3K27me3) and analyzed gene expression profiles in human adipocyte-derived stem cells under hypoxia. We identified differentially expressed genes (DEGs) and differentially methylated genes (DMGs) by hypoxia and clustered the DEGs and DMGs into four major groups. We found that each group of DEGs was predominantly associated with alterations in only one type among the three histone tri-methylations. Moreover, the four groups of DEGs were associated with different TFs and localization patterns of their predominant types of H3K4me3, H3K9me3 and H3K27me3. Our results suggest that the association of altered gene expression with prominent single-type histone tri-methylations characterized by different localization patterns and with different sets of TFs contributes to regulation of particular sets of genes, which can serve as a model for coordinated epigenetic regulation of gene expression under hypoxia.
Collapse
Affiliation(s)
- Seongyeol Lee
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Jieon Lee
- Department of Chemical Engineering, POSTECH, Pohang 37673, Republic of Korea
| | - Sehyun Chae
- Department of New Biology and Center for Plant Aging Research, Institute of Basic Science, DGIST, Daegu 42988, Republic of Korea
| | - Yunwon Moon
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Ho-Youl Lee
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Bongju Park
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Eun Gyeong Yang
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Daehee Hwang
- Department of Chemical Engineering, POSTECH, Pohang 37673, Republic of Korea.,Department of New Biology and Center for Plant Aging Research, Institute of Basic Science, DGIST, Daegu 42988, Republic of Korea
| | - Hyunsung Park
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| |
Collapse
|
78
|
Schito L, Rey S. Cell-Autonomous Metabolic Reprogramming in Hypoxia. Trends Cell Biol 2017; 28:128-142. [PMID: 29191366 DOI: 10.1016/j.tcb.2017.10.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022]
Abstract
Molecular oxygen (O2) is a universal electron acceptor that enables ATP synthesis through mitochondrial respiration in all metazoans. Consequently, hypoxia (low O2) has arisen as an organizing principle for cellular evolution, metabolism, and (patho)biology, eliciting a remarkable panoply of metabolic adaptations that trigger transcriptional, translational, post-translational, and epigenetic responses to determine cellular fitness. In this review we summarize current and emerging cell-autonomous molecular mechanisms that induce hypoxic metabolic reprogramming in health and disease.
Collapse
Affiliation(s)
- Luana Schito
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada.
| | - Sergio Rey
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| |
Collapse
|
79
|
Abstract
Alterations of genes regulating epigenetic processes are frequently found as cancer drivers and may cause widespread alterations of DNA methylation, histone modification patterns, or chromatin structure that disrupt normal patterns of gene expression. Because of the inherent reversibility of epigenetic changes, inhibitors targeting these processes are promising anticancer strategies. Small molecules targeting epigenetic regulators have been developed recently, and clinical trials of these agents are under way for hematologic malignancies and solid tumors. In this review, we describe how the writers, readers, and erasers of epigenetic marks are dysregulated in cancer and summarize the development of therapies targeting these mechanisms.
Collapse
Affiliation(s)
- Richard L Bennett
- Division of Hematology & Oncology, Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida 32606, USA;
| | - Jonathan D Licht
- Division of Hematology & Oncology, Department of Medicine, University of Florida Health Cancer Center, University of Florida, Gainesville, Florida 32606, USA;
| |
Collapse
|
80
|
Dobrynin G, McAllister TE, Leszczynska KB, Ramachandran S, Krieg AJ, Kawamura A, Hammond EM. KDM4A regulates HIF-1 levels through H3K9me3. Sci Rep 2017; 7:11094. [PMID: 28894274 PMCID: PMC5593970 DOI: 10.1038/s41598-017-11658-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/25/2017] [Indexed: 01/11/2023] Open
Abstract
Regions of hypoxia (low oxygen) occur in most solid tumours and cells in these areas are the most aggressive and therapy resistant. In response to decreased oxygen, extensive changes in gene expression mediated by Hypoxia-Inducible Factors (HIFs) contribute significantly to the aggressive hypoxic tumour phenotype. In addition to HIFs, multiple histone demethylases are altered in their expression and activity, providing a secondary mechanism to extend the hypoxic signalling response. In this study, we demonstrate that the levels of HIF-1α are directly controlled by the repressive chromatin mark, H3K9me3. In conditions where the histone demethylase KDM4A is depleted or inactive, H3K9me3 accumulates at the HIF-1α locus, leading to a decrease in HIF-1α mRNA and a reduction in HIF-1α stabilisation. Loss of KDM4A in hypoxic conditions leads to a decreased HIF-1α mediated transcriptional response and correlates with a reduction in the characteristics associated with tumour aggressiveness, including invasion, migration, and oxygen consumption. The contribution of KDM4A to the regulation of HIF-1α is most robust in conditions of mild hypoxia. This suggests that KDM4A can enhance the function of HIF-1α by increasing the total available protein to counteract any residual activity of prolyl hydroxylases.
Collapse
Affiliation(s)
- Grzegorz Dobrynin
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Tom E McAllister
- Department of Chemistry, Chemistry Research Laboratory, The University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katarzyna B Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Shaliny Ramachandran
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Akane Kawamura
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre of Human Genetics, Roosevelt Drive, The University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Chemistry Research Laboratory, The University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK.
| |
Collapse
|
81
|
Liu J, Dias K, Plagnes-Juan E, Veron V, Panserat S, Marandel L. Long-term programming effect of embryonic hypoxia exposure and high-carbohydrate diet at first feeding on glucose metabolism in juvenile rainbow trout. ACTA ACUST UNITED AC 2017; 220:3686-3694. [PMID: 28798080 DOI: 10.1242/jeb.161406] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/07/2017] [Indexed: 12/23/2022]
Abstract
Environmental conditions experienced during early life play an important role in the long-term metabolic status of individuals. The present study investigated whether hypoxia exposure [for 24 h: 2.5 mg O2 l-1 (20% dissolved O2)] during the embryonic stage alone (hypoxic history) or combined with a 5-day high-carbohydrate (60%) diet stimulus at first feeding (HC dietary history) can affect glucose metabolism later in life, i.e. in juvenile fish. After 19 weeks of growth, we observed a decrease in final body mass in fish with an HC dietary history. Feed efficiency was significantly affected by both hypoxic and HC dietary histories. After a short challenge test (5 days) performed with a 30% carbohydrate diet in juvenile trout, our results also showed that, in trout that experienced hypoxic history, mRNA levels of gluconeogenic genes in liver and glucose transport genes in both liver and muscle were significantly increased at the juvenile stage. Besides, mRNA levels of glycolytic genes were decreased in fish with an HC dietary history. Both hypoxic and dietary histories barely affected plasma metabolites or global epigenetic modifications in juvenile fish after the challenge test. In conclusion, our results demonstrated that an acute hypoxic stimulus during early development alone or combined with a hyperglucidic stimulus at first feeding can modify growth performance and glucose metabolism at the molecular level in juvenile trout.
Collapse
Affiliation(s)
- Jingwei Liu
- INRA, Université de Pau et des pays de l'Adour, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310 Saint-Pée-sur-Nivelle, France
| | - Karine Dias
- INRA, Université de Pau et des pays de l'Adour, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310 Saint-Pée-sur-Nivelle, France
| | - Elisabeth Plagnes-Juan
- INRA, Université de Pau et des pays de l'Adour, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310 Saint-Pée-sur-Nivelle, France
| | - Vincent Veron
- INRA, Université de Pau et des pays de l'Adour, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310 Saint-Pée-sur-Nivelle, France
| | - Stéphane Panserat
- INRA, Université de Pau et des pays de l'Adour, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310 Saint-Pée-sur-Nivelle, France
| | - Lucie Marandel
- INRA, Université de Pau et des pays de l'Adour, UMR1419 Nutrition Metabolism and Aquaculture, Aquapôle, F-64310 Saint-Pée-sur-Nivelle, France
| |
Collapse
|
82
|
Qiu GZ, Jin MZ, Dai JX, Sun W, Feng JH, Jin WL. Reprogramming of the Tumor in the Hypoxic Niche: The Emerging Concept and Associated Therapeutic Strategies. Trends Pharmacol Sci 2017; 38:669-686. [DOI: 10.1016/j.tips.2017.05.002] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/06/2017] [Accepted: 05/12/2017] [Indexed: 02/07/2023]
|
83
|
Maina PK, Shao P, Jia X, Liu Q, Umesalma S, Marin M, Long D, Concepción-Román S, Qi HH. Histone demethylase PHF8 regulates hypoxia signaling through HIF1α and H3K4me3. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1002-1012. [PMID: 28734980 PMCID: PMC5776039 DOI: 10.1016/j.bbagrm.2017.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 11/12/2022]
Abstract
Hypoxia through transcription factor HIF1α plays a critical role in cancer development. In prostate cancer, HIF1α interplays with androgen receptor (AR) to contribute to the progression of this disease to its lethal form—castration-resistant prostate cancer (CRPC). Hypoxia upregulates several epigenetic factors including histone demethylase KDM3A which is a critical co-factor of HIF1α. However, how histone demethylases regulate hypoxia signaling is not fully understood. Here, we report that histone demethylase PHF8 plays an essential role in hypoxia signaling. Knockdown or knockout of PHF8 by RNAi or CRISPR-Cas9 system reduced the activation of HIF1α and the induction of HIF1α target genes including KDM3A. Mechanistically, PHF8 regulates hypoxia inducible genes mainly through sustaining the level of trimethylated histone 3 lysine 4 (H3K4me3), an active mark in transcriptional regulation. The positive role of PHF8 in hypoxia signaling extended to hypoxia-induced neuroendocrine differentiation (NED), wherein PHF8 cooperates with KDM3A to regulate the expression of NED genes. Moreover, we discovered that the role of PHF8 in hypoxia signaling is associated with the presence of full-length AR in CRPC cells. Collectively, our study identified PHF8 as a novel epigenetic factor in hypoxia signaling, and the underlying regulatory mechanisms likely apply to general cancer development involving HIF1α. Therefore, targeting PHF8 can potentially be a novel therapeutic strategy in cancer therapy.
Collapse
Affiliation(s)
- Peterson Kariuki Maina
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Peng Shao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Xiongfei Jia
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Qi Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Shaikamjad Umesalma
- Department of Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Maximo Marin
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Donald Long
- Department of Biology, Southern Utah University, Cedar City, UT 84720, USA
| | | | - Hank Heng Qi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
| |
Collapse
|
84
|
Bruemmer KJ, Brewer TF, Chang CJ. Fluorescent probes for imaging formaldehyde in biological systems. Curr Opin Chem Biol 2017; 39:17-23. [PMID: 28527906 DOI: 10.1016/j.cbpa.2017.04.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/13/2017] [Accepted: 04/13/2017] [Indexed: 12/13/2022]
Abstract
Formaldehyde (FA) is a common environmental toxin but is also endogenously produced through a diverse array of essential biological processes, including mitochondrial one-carbon metabolism, metabolite oxidation, and nuclear epigenetic modifications. Its high electrophilicity enables reactivity with a wide variety of biological nucleophiles, which can be beneficial or detrimental to cellular function depending on the context. New methods that enable detection of FA in living systems can help disentangle the signal/stress dichotomy of this simplest reactive carbonyl species (RCS), and fluorescent probes for FA with high selectivity and sensitivity have emerged as promising chemical tools in this regard.
Collapse
Affiliation(s)
- Kevin J Bruemmer
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Thomas F Brewer
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | |
Collapse
|
85
|
Murn J, Shi Y. The winding path of protein methylation research: milestones and new frontiers. Nat Rev Mol Cell Biol 2017; 18:517-527. [PMID: 28512349 DOI: 10.1038/nrm.2017.35] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In 1959, while analysing the bacterial flagellar proteins, Ambler and Rees observed an unknown species of amino acid that they eventually identified as methylated lysine. Over half a century later, protein methylation is known to have a regulatory role in many essential cellular processes that range from gene transcription to signal transduction. However, the road to this now burgeoning research field was obstacle-ridden, not least because of the inconspicuous nature of the methyl mark itself. Here, we chronicle the milestone achievements and discuss the future of protein methylation research.
Collapse
Affiliation(s)
- Jernej Murn
- Department of Cell Biology, Harvard Medical School, and the Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, and the Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| |
Collapse
|
86
|
D'Ignazio L, Batie M, Rocha S. Hypoxia and Inflammation in Cancer, Focus on HIF and NF-κB. Biomedicines 2017; 5:E21. [PMID: 28536364 PMCID: PMC5489807 DOI: 10.3390/biomedicines5020021] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/02/2017] [Accepted: 05/04/2017] [Indexed: 12/25/2022] Open
Abstract
Cancer is often characterised by the presence of hypoxia and inflammation. Paramount to the mechanisms controlling cellular responses under such stress stimuli, are the transcription factor families of Hypoxia Inducible Factor (HIF) and Nuclear Factor of κ-light-chain-enhancer of activated B cells (NF-κB). Although, a detailed understating of how these transcription factors respond to their cognate stimulus is well established, it is now appreciated that HIF and NF-κB undergo extensive crosstalk, in particular in pathological situations such as cancer. Here, we focus on the current knowledge on how HIF is activated by inflammation and how NF-κB is modulated by hypoxia. We summarise the evidence for the possible mechanism behind this activation and how HIF and NF-κB function impacts cancer, focusing on colorectal, breast and lung cancer. We discuss possible new points of therapeutic intervention aiming to harness the current understanding of the HIF-NF-κB crosstalk.
Collapse
Affiliation(s)
- Laura D'Ignazio
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD15EH, UK.
| | - Michael Batie
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD15EH, UK.
| | - Sonia Rocha
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD15EH, UK.
| |
Collapse
|
87
|
Wainwright EN, Scaffidi P. Epigenetics and Cancer Stem Cells: Unleashing, Hijacking, and Restricting Cellular Plasticity. Trends Cancer 2017; 3:372-386. [PMID: 28718414 PMCID: PMC5506260 DOI: 10.1016/j.trecan.2017.04.004] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 03/30/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023]
Abstract
Epigenetic mechanisms have emerged as key players in cancer development which affect cellular states at multiple stages of the disease. During carcinogenesis, alterations in chromatin and DNA methylation resulting from genetic lesions unleash cellular plasticity and favor oncogenic cellular reprogramming. At later stages, during cancer growth and progression, additional epigenetic changes triggered by interaction with the microenvironment modulate cancer cell phenotypes and properties, and shape tumor architecture. We review here recent advances highlighting the interplay between epigenetics, genetics, and cell-to-cell signaling in cancer, with particular emphasis on mechanisms relevant for cancer stem cell formation (CSC) and function. Epigenetic regulators are one of the most commonly mutated classes of genes in cancer. During cancer initiation, mutated epigenetic regulators lead to oncogenic cellular reprogramming and promote the acquisition of uncontrolled self-renewal. The emergence of CSCs requires elaborate reorganization of the epigenome. During cancer growth, epigenetic mechanisms integrate the effect of cell-intrinsic (i.e., subclonal mutations) and cell-extrinsic (i.e., signaling from the microenvironment) changes and establish intratumoral heterogeneity, either promoting or inhibiting the CSC state. ‘Loose’ epigenetic constraints in cancer cells enhance cellular plasticity and allow reversible transitions between different phenotypic states. Enhanced cellular plasticity favors cancer cell adaptability and resistance to therapy. Modulation of epigenetic processes allows targeting of the most downstream determinants of the CSC state.
Collapse
Affiliation(s)
- Elanor N Wainwright
- Cancer Epigenetics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK.
| |
Collapse
|
88
|
Korfi K, Ali S, Heward JA, Fitzgibbon J. Follicular lymphoma, a B cell malignancy addicted to epigenetic mutations. Epigenetics 2017; 12:370-377. [PMID: 28106467 PMCID: PMC5453190 DOI: 10.1080/15592294.2017.1282587] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/07/2023] Open
Abstract
While follicular lymphoma (FL) is exquisitely responsive to immuno-chemotherapy, many patients follow a relapsing remitting clinical course driven in part by a common precursor cell (CPC) population. Advances in next generation sequencing have provided valuable insights into the genetic landscape of FL and its clonal evolution in response to therapy, implicating perturbations of epigenetic regulators as a hallmark of the disease. Recurrent mutations of histone modifiers KMT2D, CREBBP, EP300, EZH2, ARIDIA, and linker histones are likely early events arising in the CPC pool, rendering epigenetic based therapies conceptually attractive for treatment of indolent and transformed FL. This review provides a synopsis of the main epigenetic aberrations and the current efforts in development and testing of epigenetic therapies in this B cell malignancy.
Collapse
Affiliation(s)
- Koorosh Korfi
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Sara Ali
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - James A. Heward
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
89
|
The Emerging Role of Histone Demethylases in Renal Cell Carcinoma. J Kidney Cancer VHL 2017; 4:1-5. [PMID: 28725537 PMCID: PMC5515928 DOI: 10.15586/jkcvhl.2017.56] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/06/2017] [Indexed: 12/29/2022] Open
Abstract
Renal cell carcinoma (RCC), the most common kidney cancer, is responsible for more than 100,000 deaths per year worldwide. The molecular mechanism of RCC is poorly understood. Many studies have indicated that epigenetic changes such as DNA methylation, noncoding RNAs, and histone modifications are central to the pathogenesis of cancer. Histone demethylases (KDMs) play a central role in histone modifications. There is emerging evidence that KDMs such as KDM3A, KDM5C, KDM6A, and KDM6B play important roles in RCC. The available literature suggests that KDMs could promote RCC development and progression via hypoxia-mediated angiogenesis pathways. Small-molecule inhibitors of KDMs are being developed and used in preclinical studies; however, their clinical relevance is yet to be established. In this mini review, we summarize our current knowledge on the putative role of histone demethylases in RCC.
Collapse
|
90
|
Hancock R, Masson N, Dunne K, Flashman E, Kawamura A. The Activity of JmjC Histone Lysine Demethylase KDM4A is Highly Sensitive to Oxygen Concentrations. ACS Chem Biol 2017; 12:1011-1019. [PMID: 28051298 PMCID: PMC5404277 DOI: 10.1021/acschembio.6b00958] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/04/2017] [Indexed: 01/04/2023]
Abstract
The JmjC histone lysine demethylases (KDMs) are epigenetic regulators involved in the removal of methyl groups from post-translationally modified lysyl residues within histone tails, modulating gene transcription. These enzymes require molecular oxygen for catalytic activity and, as 2-oxoglutarate (2OG)-dependent oxygenases, are related to the cellular oxygen sensing HIF hydroxylases PHD2 and FIH. Recent studies have indicated that the activity of some KDMs, including the pseudogene-encoded KDM4E, may be sensitive to changing oxygen concentrations. Here, we report detailed analysis of the effect of oxygen availability on the activity of the KDM4 subfamily member KDM4A, importantly demonstrating a high level of O2 sensitivity both with isolated protein and in cells. Kinetic analysis of the recombinant enzyme revealed a high KMapp(O2) of 173 ± 23 μM, indicating that the activity of the enzyme is able to respond sensitively to a reduction in oxygen concentration. Furthermore, immunofluorescence experiments in U2OS cells conditionally overexpressing KDM4A showed that the cellular activity of KDM4A against its primary substrate, H3K9me3, displayed a graded response to depleting oxygen concentrations in line with the data obtained using isolated protein. These results suggest that KDM4A possesses the potential to act as an oxygen sensor in the context of chromatin modifications, with possible implications for epigenetic regulation in hypoxic disease states. Importantly, this correlation between the oxygen sensitivity of the catalytic activity of KDM4A in biochemical and cellular assays demonstrates the utility of biochemical studies in understanding the factors contributing to the diverse biological functions and varied activity of the 2OG oxygenases.
Collapse
Affiliation(s)
- Rebecca
L Hancock
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust
Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Norma Masson
- Target Discovery Institute, NDM Research Building, University
of Oxford, Roosevelt
Drive, Oxford OX3 7BN, United Kingdom
| | - Kate Dunne
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust
Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Emily Flashman
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Akane Kawamura
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust
Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| |
Collapse
|
91
|
Alivand MR, Soheili ZS, Pornour M, Solali S, Sabouni F. Novel Epigenetic Controlling of Hypoxia Pathway Related to Overexpression and Promoter Hypomethylation of TET1 and TET2 in RPE Cells. J Cell Biochem 2017; 118:3193-3204. [PMID: 28252217 DOI: 10.1002/jcb.25965] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 02/28/2017] [Indexed: 12/19/2022]
Abstract
CpG methylation of DNA takes part in a specific epigenetic memory that plays crucial roles in the differentiation and abnormality of the cells. The methylation pattern aberration of genomes is affected in three ways, namely DNA methyltransferase (DNMT), ten-eleven translocation (TET), and methyl-binding domain (MBD) proteins. Of these, TET enzymes have recently been demonstrated to be master modifier enzymes in the DNA methylation process. Additionally, recent studies emphasize that not only epigenetic phenomena play a role in controlling hypoxia pathway, but the hypoxia condition also triggers hypomethylation of genomes that may help with the expression of hypoxia pathway genes. In this study, we suggested that TET1 and TET2 could play a role in the demethylation of genomes under chemical hypoxia conditions. Herein, the evaluating methylation status and mRNA expression of mentioned genes were utilized through real-time PCR and methylation-specific PCR (MSP), respectively. Our results showed that TET1 and TET2 genes were overexpressed (P < 0.05) under chemical hypoxia conditions in Retinal Pigment Epithelial (RPE) cells, whereas the promoter methylation status of them were hypomethylated in the same condition. Therefore, chemical hypoxia not only causes overexpression of TET1 and TET2 but also could gradually do promoter demethylation of same genes. This is the first study to show the relationship between epigenetics and the expression of mentioned genes related to hypoxia pathways. Furthermore, it seems that these associations in RPE cells are subjected to chemical hypoxia as a mechanism that could play a crucial role in methylation pattern changes of hypoxia-related diseases such as cancer and ischemia. J. Cell. Biochem. 118: 3193-3204, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra-Soheila Soheili
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Saeed Solali
- Department of Hematology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Sabouni
- Department of Molecular Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| |
Collapse
|
92
|
Matilainen O, Quirós PM, Auwerx J. Mitochondria and Epigenetics - Crosstalk in Homeostasis and Stress. Trends Cell Biol 2017; 27:453-463. [PMID: 28274652 DOI: 10.1016/j.tcb.2017.02.004] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/07/2017] [Accepted: 02/12/2017] [Indexed: 12/22/2022]
Abstract
Through epigenetic mechanisms cells integrate environmental stimuli to fine-tune gene expression levels. Mitochondrial function is essential to provide the intermediate metabolites necessary to generate and modify epigenetic marks in the nucleus, which in turn can regulate the expression of mitochondrial proteins. In this review we summarize the function of mitochondria in the regulation of epigenetic mechanisms as a new aspect of mitonuclear communication. We focus in particular on the most common epigenetic modifications - histone acetylation and histone and DNA methylation. We also discuss the emerging field of mitochondrial DNA (mtDNA) methylation, whose physiological role remains unknown. Finally, we describe the essential role of some histone modifications in regulating the mitochondrial unfolded protein response (UPRmt) and the mitochondrial stress-dependent lifespan extension.
Collapse
Affiliation(s)
- Olli Matilainen
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Pedro M Quirós
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| |
Collapse
|
93
|
Perspectivas moleculares en cardiopatía hipertrófica: abordaje epigenético desde la modificación de la cromatina. REVISTA COLOMBIANA DE CARDIOLOGÍA 2017. [DOI: 10.1016/j.rccar.2016.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
94
|
Connor JR, Patton SM, Oexle K, Allen RP. Iron and restless legs syndrome: treatment, genetics and pathophysiology. Sleep Med 2016; 31:61-70. [PMID: 28057495 DOI: 10.1016/j.sleep.2016.07.028] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/22/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022]
Abstract
In this article, we review the original findings from MRI and autopsy studies that demonstrated brain iron status is insufficient in individuals with restless legs syndrome (RLS). The concept of deficient brain iron status is supported by proteomic studies from cerebrospinal fluid (CSF) and from the clinical findings where intervention with iron, either dietary or intravenous, can improve RLS symptoms. Therefore, we include a section on peripheral iron status and how peripheral status may influence both the RLS symptoms and treatment strategy. Given the impact of iron in RLS, we have evaluated genetic data to determine if genes are directly involved in iron regulatory pathways. The result was negative. In fact, even the HFE mutation C282Y could not be shown to have a protective effect. Lastly, a consistent finding in conditions of low iron is increased expression of proteins in the hypoxia pathway. Although there is lack of clinical data that RLS patients are hypoxic, there are intriguing observations that environmental hypoxic conditions worsen RLS symptoms; in this chapter we review very compelling data for activation of hypoxic pathways in the brain in RLS patients. In general, the data in RLS point to a pathophysiology that involves decreased acquisition of iron by cells in the brain. Whether the decreased ability is genetically driven, activation of pathways (eg, hypoxia) that are designed to limit cellular uptake is unknown at this time; however, the data strongly support a functional rather than structural defect in RLS, suggesting that an effective treatment is possible.
Collapse
Affiliation(s)
- James R Connor
- Department of Neurosurgery, Penn State Hershey Medical Center, Hershey, PA, USA.
| | - Stephanie M Patton
- Department of Neurosurgery, Penn State Hershey Medical Center, Hershey, PA, USA
| | - Konrad Oexle
- Institut für Humangenetik, Technische Universität, Munich, Germany
| | - Richard P Allen
- The Johns Hopkins University, Dep of neuroloy, Baltimore, MD USA
| |
Collapse
|
95
|
HIF-KDM3A-MMP12 regulatory circuit ensures trophoblast plasticity and placental adaptations to hypoxia. Proc Natl Acad Sci U S A 2016; 113:E7212-E7221. [PMID: 27807143 DOI: 10.1073/pnas.1612626113] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The hemochorial placenta develops from the coordinated multilineage differentiation of trophoblast stem (TS) cells. An invasive trophoblast cell lineage remodels uterine spiral arteries, facilitating nutrient flow, failure of which is associated with pathological conditions such as preeclampsia, intrauterine growth restriction, and preterm birth. Hypoxia plays an instructive role in influencing trophoblast cell differentiation and regulating placental organization. Key downstream hypoxia-activated events were delineated using rat TS cells and tested in vivo, using trophoblast-specific lentiviral gene delivery and genome editing. DNA microarray analyses performed on rat TS cells exposed to ambient or low oxygen and pregnant rats exposed to ambient or hypoxic conditions showed up-regulation of genes characteristic of an invasive/vascular remodeling/inflammatory phenotype. Among the shared up-regulated genes was matrix metallopeptidase 12 (MMP12). To explore the functional importance of MMP12 in trophoblast cell-directed spiral artery remodeling, we generated an Mmp12 mutant rat model using transcription activator-like nucleases-mediated genome editing. Homozygous mutant placentation sites showed decreased hypoxia-dependent endovascular trophoblast invasion and impaired trophoblast-directed spiral artery remodeling. A link was established between hypoxia/HIF and MMP12; however, evidence did not support Mmp12 as a direct target of HIF action. Lysine demethylase 3A (KDM3A) was identified as mediator of hypoxia/HIF regulation of Mmp12 Knockdown of KDM3A in rat TS cells inhibited the expression of a subset of the hypoxia-hypoxia inducible factor (HIF)-dependent transcripts, including Mmp12, altered H3K9 methylation status, and decreased hypoxia-induced trophoblast cell invasion in vitro and in vivo. The hypoxia-HIF-KDM3A-MMP12 regulatory circuit is conserved and facilitates placental adaptations to environmental challenges.
Collapse
|
96
|
Epigenetic Regulation of SNAP25 Prevents Progressive Glutamate Excitotoxicty in Hypoxic CA3 Neurons. Mol Neurobiol 2016; 54:6133-6147. [PMID: 27699604 DOI: 10.1007/s12035-016-0156-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/22/2016] [Indexed: 01/31/2023]
Abstract
Exposure to global hypoxia and ischemia has been reported to cause neurodegeneration in the hippocampus with CA3 neurons. This neuronal damage is progressive during the initial phase of exposure but maintains a plateau on prolonged exposure. The present study on Sprague Dawley rats aimed at understanding the underlying molecular and epigenetic mechanisms that lead to hypoxic adaptation of CA3 neurons on prolonged exposure to a global hypoxia. Our results show stagnancy in neurodegeneration in CA3 region beyond 14 days of chronic exposure to hypobaria simulating an altitude of 25,000 ft. Despite increased synaptosomal glutamate and higher expression of NR1 subunit of NMDA receptors, we observed decrease in post-synaptic density and accumulation of synaptic vesicles at the pre-synaptic terminals. Molecular investigations involving western blot and real-time PCR showed duration-dependent decrease in the expression of SNAP-25 resulting in reduced vesicular docking and synaptic remodeling. ChIP assays for epigenetic factors showed decreased expression of H3K9Ac and H3K14Ac resulting in SNAP-25 promoter silencing during prolonged hypoxia. Administration of sodium butyrate, a non-specific HDAC inhibitor, during 21 days hypoxic exposure prevented SNAP-25 downregulation but increased CA3 neurodegeneration. This epigenetic regulation of SNAP-25 promoter was independent of increased DNMT3b expression and promoter methylation. Our findings provide a novel insight into epigenetic factors-mediated synaptic remodeling to prevent excitotoxic neurodegeneration on prolonged exposure to global hypobaric hypoxia.
Collapse
|
97
|
Greville G, McCann A, Rudd PM, Saldova R. Epigenetic regulation of glycosylation and the impact on chemo-resistance in breast and ovarian cancer. Epigenetics 2016; 11:845-857. [PMID: 27689695 DOI: 10.1080/15592294.2016.1241932] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glycosylation is one of the most fundamental posttranslational modifications in cellular biology and has been shown to be epigenetically regulated. Understanding this process is important as epigenetic therapies such as those using DNA methyltransferase inhibitors are undergoing clinical trials for the treatment of ovarian and breast cancer. Previous work has demonstrated that altered glycosylation patterns are associated with aggressive disease in women presenting with breast and ovarian cancer. Moreover, the tumor microenvironment of hypoxia results in globally altered DNA methylation and is associated with aggressive cancer phenotypes and chemo-resistance, a feature integral to many cancers. There is sparse knowledge on the impact of these therapies on glycosylation. Moreover, little is known about the efficacy of DNA methyltransferase inhibitors in hypoxic tumors. In this review, we interrogate the impact that hypoxia and epigenetic regulation has on cancer cell glycosylation in relation to resultant tumor cell aggressiveness and chemo-resistance.
Collapse
Affiliation(s)
- Gordon Greville
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
| | - Amanda McCann
- b UCD School of Medicine, College of Health and Agricultural Science, University College Dublin , UCD, Belfield, Dublin , Ireland.,c UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , UCD, Belfield, Dublin , Ireland
| | - Pauline M Rudd
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
| | - Radka Saldova
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
| |
Collapse
|
98
|
Manente AG, Pinton G, Zonca S, Tavian D, Habib T, Jithesh PV, Fennell D, Nilsson S, Moro L. KDM6B histone demethylase is an epigenetic regulator of estrogen receptor β expression in human pleural mesothelioma. Epigenomics 2016; 8:1227-38. [PMID: 27529370 DOI: 10.2217/epi-2016-0025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
AIM To assess the correlation between KDM6B and estrogen receptor β (ERβ) expression in malignant pleural mesothelioma (MPM). MATERIALS & METHODS We evaluated gene expression by in silico analysis of microarray data, real-time PCR and western blot in MPM tumors and cell lines. RESULTS & CONCLUSION We report a strong positive correlation between the expression of KDM6B and ERβ in MPM tumors and cell lines. We describe that, in hypoxia, the HIF2α-KDM6B axis induces an epithelioid morphology and ERβ expression in biphasic MPM cells with estrogen receptor-negative phenotype. Reduced histone H3K27 tri-methylation confirms KDM6B activity under hypoxic conditions. Importantly, cells treated during reoxygenation with the selective ERβ agonist, KB9520, maintain ERβ expression and the less aggressive phenotype acquired in hypoxia.
Collapse
Affiliation(s)
- Arcangela G Manente
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Lgo Donegani 2, 28100 Novara, Italy
| | | | - Sara Zonca
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Lgo Donegani 2, 28100 Novara, Italy
| | - Daniela Tavian
- Laboratory of Cellular Biochemistry & Molecular Biology, CRIBENS, Catholic University of the Sacred Heart, 20145 Milan, Italy
| | - Tanwir Habib
- Sidra Medical & Research Center, P.O. Box 26999 Doha, Qatar
| | | | - Dean Fennell
- University of Leicester & Leicester University Hospitals, LE1 9HN, Leicester, UK
| | - Stefan Nilsson
- Department of Biosciences & Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
| | - Laura Moro
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Lgo Donegani 2, 28100 Novara, Italy
| |
Collapse
|
99
|
Lai KP, Li JW, Chan CYS, Chan TF, Yuen KWY, Chiu JMY. Transcriptomic alterations in Daphnia magna embryos from mothers exposed to hypoxia. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 177:454-463. [PMID: 27399157 DOI: 10.1016/j.aquatox.2016.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Hypoxia occurs when dissolved oxygen (DO) falls below 2.8mgL(-1) in aquatic environments. It can cause trans-generational effects not only in fish, but also in the water fleas Daphnia. In this study, transcriptome sequencing analysis was employed to identify transcriptomic alterations induced by hypoxia in embryos of Daphnia magna, with an aim to investigate the mechanism underlying the trans-generational effects caused by hypoxia in Daphnia. The embryos (F1) were collected from adults (F0) that were previously exposed to hypoxia (or normoxia) for their whole life. De novo transcriptome assembly identified 18270 transcripts that were matched to the UniProtKB/Swiss-Prot database and resulted in 7419 genes. Comparative transcriptome analysis showed 124 differentially expressed genes, including 70 up- and 54 down-regulated genes under hypoxia. Gene ontology analysis further highlighted three clusters of genes which revealed acclimatory changes of haemoglobin, suppression in vitellogenin gene family and histone modifications. Specifically, the expressions of histone H2B, H3, H4 and histone deacetylase 4 (HDAC4) were deregulated. This study suggested that trans-generational effects of hypoxia on Daphnia may be mediated through epigenetic regulations of histone modifications.
Collapse
Affiliation(s)
- Keng-Po Lai
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong
| | - Jing-Woei Li
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | | | - Ting-Fung Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | | | | |
Collapse
|
100
|
Nowak RP, Tumber A, Johansson C, Che KH, Brennan P, Owen D, Oppermann U. Advances and challenges in understanding histone demethylase biology. Curr Opin Chem Biol 2016; 33:151-9. [PMID: 27371875 DOI: 10.1016/j.cbpa.2016.06.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/09/2016] [Accepted: 06/17/2016] [Indexed: 01/08/2023]
Abstract
Within the last decade we have witnessed significant progress in the field of chromatin methylation, ranging from the discovery that chromatin methylation is reversible, to the identification of two classes of oxidative chromatin demethylases. Multiple genetic and cellular studies emphasize the role of members of the amine oxidase and 2-oxoglutarate oxygenase enzyme families involved in methyl-lysine in physiology and disease. Advances in understanding of the underlying biochemistry have resulted in development of first series of clinical inhibitors and tool compounds which continue to resolve and help understand the complex relationships between chromatin modification, control of gene expression and metabolic states.
Collapse
Affiliation(s)
- Radoslaw P Nowak
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Oxford OX3 7LD, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK; Target Discovery Institute, University of Oxford, OX3 7FZ, UK
| | - Catrine Johansson
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Oxford OX3 7LD, UK; Department of Chemistry, University of Oxford, OX1 3TA, UK
| | - Ka Hing Che
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Oxford OX3 7LD, UK
| | - Paul Brennan
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK; Target Discovery Institute, University of Oxford, OX3 7FZ, UK
| | - Dafydd Owen
- Pfizer Worldwide Medicinal Chemistry, 610 Main Street, Cambridge, MA 02139, USA
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Oxford OX3 7LD, UK.
| |
Collapse
|