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Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024; 98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is intrinsic to tumours and contributes to malignancy and metastasis while hindering the efficiency of existing treatments. Epigenetic mechanisms play a crucial role in the regulation of hypoxic cancer cell programs, both in the initial phases of sensing the decrease in oxygen levels and during adaptation to chronic lack of oxygen. During the latter, the epigenetic regulation of tumour biology intersects with hypoxia-sensitive transcription factors in a complex network of gene regulation that also involves metabolic reprogramming. Here, we review the current literature on the epigenetic control of gene programs in hypoxic cancer cells. We highlight common themes and features of such epigenetic remodelling and discuss their relevance for the development of therapeutic strategies.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium; KU Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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2
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Nakagawa R, Llorian M, Varsani-Brown S, Chakravarty P, Camarillo JM, Barry D, George R, Blackledge NP, Duddy G, Kelleher NL, Klose RJ, Turner M, Calado DP. Epi-microRNA mediated metabolic reprogramming ensures affinity maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551250. [PMID: 37609190 PMCID: PMC10441342 DOI: 10.1101/2023.07.31.551250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
To increase antibody affinity against pathogens, positively selected GC-B cells initiate cell division in the light zone (LZ) of germinal centres (GCs). Among those, higher-affinity clones migrate to the dark zone (DZ) and vigorously proliferate by relying on oxidative phosphorylation (OXPHOS). However, it remains unknown how positively selected GC-B cells adapt their metabolism for cell division in the glycolysis-dominant, cell cycle arrest-inducing, hypoxic LZ microenvironment. Here, we show that microRNA (miR)-155 mediates metabolic reprogramming during positive selection to protect high-affinity clones. Transcriptome examination and mass spectrometry analysis revealed that miR-155 regulates H3K36me2 levels by directly repressing hypoxia-induced histone lysine demethylase, Kdm2a. This is indispensable for enhancing OXPHOS through optimizing the expression of vital nuclear mitochondrial genes under hypoxia. The miR-155-Kdm2a interaction is crucial to prevent excessive production of reactive oxygen species and apoptosis. Thus, miR-155-mediated epigenetic regulation promotes mitochondrial fitness in high-affinity clones, ensuring their expansion and consequently affinity maturation.
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3
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Feng S, DeGrey SP, Guédot C, Schoville SD, Pool JE. Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547576. [PMID: 37461625 PMCID: PMC10349955 DOI: 10.1101/2023.07.03.547576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Biological invasions carry substantial practical and scientific importance, and represent natural evolutionary experiments on contemporary timescales. Here, we investigated genomic diversity and environmental adaptation of the crop pest Drosophila suzukii using whole-genome sequencing data and environmental metadata for 29 population samples from its native and invasive range. Through a multifaceted analysis of this population genomic data, we increase our understanding of the D. suzukii genome, its diversity and its evolution, and we identify an appropriate genotype-environment association pipeline for our data set. Using this approach, we detect genetic signals of local adaptation associated with nine distinct environmental factors related to altitude, wind speed, precipitation, temperature, and human land use. We uncover unique functional signatures for each environmental variable, such as a prevalence of cuticular genes associated with annual precipitation. We also infer biological commonalities in the adaptation to diverse selective pressures, particularly in terms of the apparent contribution of nervous system evolution to enriched processes (ranging from neuron development to circadian behavior) and to top genes associated with all nine environmental variables. Our findings therefore depict a finer-scale adaptive landscape underlying the rapid invasion success of this agronomically important species.
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Affiliation(s)
- Siyuan Feng
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel P. DeGrey
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christelle Guédot
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
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4
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Elcocks H, Brazel AJ, McCarron KR, Kaulich M, Husnjak K, Mortiboys H, Clague MJ, Urbé S. FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels. EMBO J 2023; 42:e112799. [PMID: 37102372 PMCID: PMC10308357 DOI: 10.15252/embj.2022112799] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/17/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023] Open
Abstract
Selective autophagy of mitochondria, mitophagy, is linked to mitochondrial quality control and as such is critical to a healthy organism. We have used a CRISPR/Cas9 approach to screen human E3 ubiquitin ligases for influence on mitophagy under both basal cell culture conditions and upon acute mitochondrial depolarization. We identify two cullin-RING ligase substrate receptors, VHL and FBXL4, as the most profound negative regulators of basal mitophagy. We show that these converge, albeit via different mechanisms, on control of the mitophagy adaptors BNIP3 and BNIP3L/NIX. FBXL4 restricts NIX and BNIP3 levels via direct interaction and protein destabilization, while VHL acts through suppression of HIF1α-mediated transcription of BNIP3 and NIX. Depletion of NIX but not BNIP3 is sufficient to restore mitophagy levels. Our study contributes to an understanding of the aetiology of early-onset mitochondrial encephalomyopathy that is supported by analysis of a disease-associated mutation. We further show that the compound MLN4924, which globally interferes with cullin-RING ligase activity, is a strong inducer of mitophagy, thus providing a research tool in this context and a candidate therapeutic agent for conditions linked to mitochondrial dysfunction.
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Affiliation(s)
- Hannah Elcocks
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Ailbhe J Brazel
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
- Present address:
Department of BiologyMaynooth UniversityMaynoothIreland
| | - Katy R McCarron
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Manuel Kaulich
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
| | - Koraljka Husnjak
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Michael J Clague
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Sylvie Urbé
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
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5
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Collier H, Albanese A, Kwok CS, Kou J, Rocha S. Functional crosstalk between chromatin and hypoxia signalling. Cell Signal 2023; 106:110660. [PMID: 36990334 DOI: 10.1016/j.cellsig.2023.110660] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Eukaryotic genomes are organised in a structure called chromatin, comprising of DNA and histone proteins. Chromatin is thus a fundamental regulator of gene expression, as it offers storage and protection but also controls accessibility to DNA. Sensing and responding to reductions in oxygen availability (hypoxia) have recognised importance in both physiological and pathological processes in multicellular organisms. One of the main mechanisms controlling these responses is control of gene expression. Recent findings in the field of hypoxia have highlighted how oxygen and chromatin are intricately linked. This review will focus on mechanisms controlling chromatin in hypoxia, including chromatin regulators such as histone modifications and chromatin remodellers. It will also highlight how these are integrated with hypoxia inducible factors and the knowledge gaps that persist.
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Affiliation(s)
- Harry Collier
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Adam Albanese
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Chun-Sui Kwok
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Jiahua Kou
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Sonia Rocha
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom.
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6
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Zuo Y, Zhan L, Wen H, Xue J, Tan Y, Sun W, Xu E. Stabilization of nuclear β-catenin by inhibiting KDM2A mediates cerebral ischemic tolerance. FASEB J 2023; 37:e22796. [PMID: 36723950 DOI: 10.1096/fj.202201657] [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: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 02/02/2023]
Abstract
Hypoxic postconditioning (HPC) with 8% oxygen increases nuclear accumulation of β-catenin through activating the classical Wnt pathway, thereby alleviating transient global cerebral ischemia (tGCI)-induced neuronal damage in the hippocampal CA1 subregion of adult rats. However, little is understood about the regulatory mechanism of nuclear β-catenin in HPC-mediated cerebral ischemic tolerance. Although lysine(K)-specific demethylase 2A (KDM2A) has been known as a crucial regulator of nuclear β-catenin destabilization, whether it plays an important role through modulating nuclear β-catenin in cerebral ischemic tolerance induced by HPC remains unknown. In this study, we explored the molecular mechanism of stabilizing nuclear β-catenin by inhibiting KDM2A-mediated demethylation in the HPC-offered neuroprotection against tGCI. In addition, we confirmed that nuclear methylated-β-catenin in CA1 decreased and nuclear β-catenin turnover increased after tGCI, which were reversed by HPC. The administration with methyltransferase inhibitor AdOx abrogated HPC-induced methylation and stabilization of nuclear β-catenin in CA1, as well as the neuroprotection against tGCI. Notably, HPC downregulated the expression of KDM2A in CA1 and reduced the interaction between KDM2A and β-catenin in the nucleus after tGCI. The knockdown of KDM2A with small-interfering RNA could upregulate nuclear methylated-β-catenin and stabilize β-catenin, thereby increasing survivin in CA1 and improving the cognitive function of rats after tGCI. Opposite results were observed by the administration of KDM2A-carried adenovirus vector. Furthermore, we demonstrated that KDM2A mediates the demethylation of nuclear β-catenin through jumonji C (JmjC) domain of KDM2A in HEK-293T and SH-SY5Y cells. Our data support that the inhibition of KDM2A-mediated demethylation of nuclear β-catenin contributes to HPC-induced neuroprotection against tGCI.
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Affiliation(s)
- Yunyan Zuo
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lixuan Zhan
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Haixia Wen
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Neurology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jiahui Xue
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yafu Tan
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Weiwen Sun
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - En Xu
- Department of Neurology, Institute of Neurosciences, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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Abstract
Hypoxia is defined as a cellular stress condition caused by a decrease in oxygen below physiologically normal levels. Cells in the core of a rapidly growing solid tumor are faced with the challenge of inadequate supply of oxygen through the blood, owing to improper vasculature inside the tumor. This hypoxic microenvironment inside the tumor initiates a gene expression program that alters numerous signaling pathways, allowing the cancer cell to eventually evade adverse conditions and attain a more aggressive phenotype. A multitude of studies covering diverse aspects of gene regulation has tried to uncover the mechanisms involved in hypoxia-induced tumorigenesis. The role of epigenetics in executing widespread and dynamic changes in gene expression under hypoxia has been gaining an increasing amount of support in recent years. This chapter discusses, in detail, various epigenetic mechanisms driving the cellular response to hypoxia in cancer.
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Affiliation(s)
- Deepak Pant
- Epigenetics and RNA Processing Lab (ERPL), Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Srinivas Abhishek Mutnuru
- Epigenetics and RNA Processing Lab (ERPL), Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Sanjeev Shukla
- Epigenetics and RNA Processing Lab (ERPL), Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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8
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Zhitkovich A. Ascorbate: antioxidant and biochemical activities and their importance for in vitro models. Arch Toxicol 2021; 95:3623-3631. [PMID: 34596731 DOI: 10.1007/s00204-021-03167-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022]
Abstract
Ascorbate has many biological activities that involve fundamental cellular functions such as gene expression, differentiation, and redox homeostasis. Biochemically, it serves as a cofactor for a large family of dioxygenases (> 60 members) which control transcription, formation of extracellular matrix, and epigenetic processes of histone and DNA demethylation. Ascorbate is also a major antioxidant acting as a very effective scavenger of primary reactive oxygen species. Reduction of Fe(III) by ascorbate is important for cellular uptake of iron via DMT1. Cell culture models are extensively used in toxicology and pharmacology for mechanistic studies of nutrients, drugs and other xenobiotics. High-throughput screens in vitro, such as a large-scale Tox21 program in the US, offers opportunities to assess hazardous properties of a vast and growing number of industrial chemicals. However, cells in typical cultures are severely deficient in ascorbate, raising concerns about their ability to accurately recapitulate toxic and other responses in vivo. Scarcity of ascorbate and a frequently unrecognized use of media with its thiol substitute alters stress sensitivity of cells in different directions. Remediation of ascorbate deficiency in tissue culture restores the physiological state of many cellular processes and it should improve a currently limited toxicity predictability of in vitro bioassays.
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Affiliation(s)
- Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Room 507, Providence, RI, 02912, USA.
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9
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Daly LA, Brownridge PJ, Batie M, Rocha S, Sée V, Eyers CE. Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α. Sci Signal 2021; 14:eabf6685. [PMID: 34285132 DOI: 10.1126/scisignal.abf6685] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cellular adaptation to low-oxygen environments is mediated in part by the hypoxia-inducible factors (HIFs). Like other transcription factors, the stability and transcriptional activity of HIFs-and consequently, the hypoxic response-are regulated by post-translational modifications (PTMs) and changes in protein-protein interactions. Our current understanding of PTM-mediated regulation of HIFs is primarily based on in vitro protein fragment-based studies typically validated in fragment-expressing cells treated with hypoxia-mimicking compounds. Here, we used immunoprecipitation-based mass spectrometry to characterize the PTMs and binding partners for full-length HIF-1α and HIF-2α under normoxic (21% oxygen) and hypoxic (1% oxygen) conditions. Hypoxia substantially altered the complexity and composition of the HIFα protein interaction networks, particularly for HIF-2α, with the hypoxic networks of both isoforms being enriched for mitochondrial proteins. Moreover, both HIFα isoforms were heavily covalently modified. We identified ~40 PTM sites composed of 13 different types of modification on both HIFα isoforms, including multiple cysteine modifications and an unusual phosphocysteine. More than 80% of the PTMs identified were not previously known and about half exhibited oxygen dependency. We further characterized an evolutionarily conserved phosphorylation of Ser31 in HIF-1α as a regulator of its transcriptional function, and we propose functional roles for Thr406, Thr528, and Ser581 in HIF-2α. These data will help to delineate the different physiological roles of these closely related isoforms in fine-tuning the hypoxic response.
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Affiliation(s)
- Leonard A Daly
- Department of Biochemistry and System Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
- Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
| | - Philip J Brownridge
- Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
| | - Michael Batie
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Sonia Rocha
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Violaine Sée
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- Centre for Cell Imaging, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry and System Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- Centre for Proteome Research, University of Liverpool, Liverpool L69 7ZB, UK
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10
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Liu X, Li J, Wang Z, Meng J, Wang A, Zhao X, Xu Q, Cai Z, Hu Z. KDM2A Targets PFKFB3 for Ubiquitylation to Inhibit the Proliferation and Angiogenesis of Multiple Myeloma Cells. Front Oncol 2021; 11:653788. [PMID: 34079757 PMCID: PMC8165180 DOI: 10.3389/fonc.2021.653788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
The lysine demethylase KDM2A (also known as JHDM1A or FBXL11) demethylates histone H3 at lysine K36 which lead to epigenetic regulation of cell proliferation and tumorigenesis. However, many biological processes are mediated by KDM2A independently by its histone demethylation activity. In the present study, we aimed to characterize the functional significance of KDM2A in multiple myeloma (MM) disease progression. Specifically, we defined that one of the key enzymes of glycolysis PFKFB3 (6-phosphofructo-2-kinase) is ubiquitylated by KDM2A which suppresses MM cell proliferation. Previous study showed that KDM2A and PFKFB3 promoted angiogenesis in various tumor cells. We further reveal that KDM2A targets PFKFB3 for ubiquitination and degradation to inhibit angiogenesis. Several angiogenic cytokines are also downregulated in MM. Clinically, MM patients with low KDM2A and high PFKFB3 levels have shown worse prognosis. These results reveal a novel function of KDM2A through ubiquitin ligase activity by targeting PFKFB3 to induce proliferation, glycolysis and angiogenesis in MM cells. The data provides a new potential mechanism and strategy for MM treatment.
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Affiliation(s)
- Xinling Liu
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jiaqiu Li
- Department of Oncology, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Zhanju Wang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jie Meng
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Aihong Wang
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xiaofei Zhao
- Department of Dermatology, Weifang Hospital of Traditional Chinese Medicine, Weifang, China
| | - Qilu Xu
- Department of Hematology, The First Affiliated Hospital, Weifang Medical University, Weifang, China
| | - Zhen Cai
- Department of Hematology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhenbo Hu
- Department of Hematology, Laboratory for Stem Cell and Regenerative Medicine, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang, China
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11
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Sterling J, Menezes SV, Abbassi RH, Munoz L. Histone lysine demethylases and their functions in cancer. Int J Cancer 2021; 148:2375-2388. [PMID: 33128779 DOI: 10.1002/ijc.33375] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022]
Abstract
Histone lysine demethylases (KDMs) are enzymes that remove the methylation marks on lysines in nucleosomes' histone tails. These changes in methylation marks regulate gene transcription during both development and malignant transformation. Depending on which lysine residue is targeted, the effect of a given KDM on gene transcription can be either activating or repressing, and KDMs can regulate the expression of both oncogenes and tumour suppressors. Thus, the functions of KDMs can be regarded as both oncogenic and tumour suppressive, contingent on cell context and the enzyme isoform. Finally, KDMs also demethylate nonhistone proteins and have a variety of demethylase-independent functions. These epigenetic and other mechanisms that KDMs control make them important regulators of malignant tumours. Here, we present an overview of eight KDM subfamilies, their most-studied lysine targets and selected recent data on their roles in cancer stem cells, tumour aggressiveness and drug tolerance.
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Affiliation(s)
- Jayden Sterling
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharleen V Menezes
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ramzi H Abbassi
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Lenka Munoz
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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12
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KDM2B Overexpression Facilitates Lytic De Novo KSHV Infection by Inducing AP-1 Activity Through Interaction with the SCF E3 Ubiquitin Ligase Complex. J Virol 2021; 95:JVI.00331-21. [PMID: 33692209 PMCID: PMC8139688 DOI: 10.1128/jvi.00331-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
It is still largely unknown what host factors are involved in controlling the expression of the lytic viral gene RTA during primary infection, which determines if Kaposi's sarcoma-associated herpesvirus (KSHV) establishes latent or lytic infection. We have recently identified the histone demethylase KDM2B as a repressor of RTA expression during both de novo KSHV infection and latency based on an epigenetic factor siRNA screen. Here, we report that surprisingly, KDM2B overexpression can promote lytic de novo infection by using a mechanism that differs from what is needed for its repressor function. Our study revealed that while the DNA-binding and demethylase activities of KDM2B linked to its transcription repressive function are dispensable, its C-terminal F-box and LRR domains are required for the lytic infection-inducing function of KDM2B. We found that overexpressed KDM2B increases the half-life of the AP-1 subunit c-Jun protein and induces the AP-1 signaling pathway. This effect is dependent upon the binding of KDM2B to the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase complex via its F-box domain. Importantly, the inhibition of AP-1 reduces KDM2B-mediated lytic de novo KSHV infection. Overall, our findings indicate that KDM2B may induce the degradation of some host factors by using the SCF complex resulting in the enrichment of c-Jun. This leads to increased AP-1 transcriptional activity, which facilitates lytic gene expression following de novo infection interfering with the establishment of viral latency.SignificanceThe expression of epigenetic factors is often dysregulated in cancers or upon specific stress signals, which often results in a display of non-canonical functions of the epigenetic factors that are independent from their chromatin-modifying roles. We have previously demonstrated that KDM2B normally inhibits KSHV lytic cycle using its histone demethylase activity. Surprisingly, we found that KDM2B overexpression can promote lytic de novo infection, which does not require its histone demethylase or DNA-binding functions. Instead, KDM2B uses the SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase complex to induce AP-1 transcriptional activity, which promotes lytic gene expression. This is the first report that demonstrates a functional link between SFCKDM2B and AP-1 in the regulation of KSHV lytic cycle.
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13
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Clinical Manifestations and Epigenetic Regulation of Oral Herpesvirus Infections. Viruses 2021; 13:v13040681. [PMID: 33920978 PMCID: PMC8071331 DOI: 10.3390/v13040681] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
The oral cavity is often the first site where viruses interact with the human body. The oral epithelium is a major site of viral entry, replication and spread to other cell types, where chronic infection can be established. In addition, saliva has been shown as a primary route of person-to-person transmission for many viruses. From a clinical perspective, viral infection can lead to several oral manifestations, ranging from common intraoral lesions to tumors. Despite the clinical and biological relevance of initial oral infection, little is known about the mechanism of regulation of the viral life cycle in the oral cavity. Several viruses utilize host epigenetic machinery to promote their own life cycle. Importantly, viral hijacking of host chromatin-modifying enzymes can also lead to the dysregulation of host factors and in the case of oncogenic viruses may ultimately play a role in promoting tumorigenesis. Given the known roles of epigenetic regulation of viral infection, epigenetic-targeted antiviral therapy has been recently explored as a therapeutic option for chronic viral infection. In this review, we highlight three herpesviruses with known roles in oral infection, including herpes simplex virus type 1, Epstein–Barr virus and Kaposi’s sarcoma-associated herpesvirus. We focus on the respective oral clinical manifestations of these viruses and their epigenetic regulation, with a specific emphasis on the viral life cycle in the oral epithelium.
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Gene transcription and chromatin regulation in hypoxia. Biochem Soc Trans 2021; 48:1121-1128. [PMID: 32369557 PMCID: PMC7329336 DOI: 10.1042/bst20191106] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 12/30/2022]
Abstract
Oxygen sensing is an essential feature of metazoan biology and reductions in oxygen availability (hypoxia) have both physiological and pathophysiological implications. Co-ordinated mechanisms have evolved for sensing and responding to hypoxia, which involve diverse biological outputs, with the main aim of restoring oxygen homeostasis. This includes a dynamic gene transcriptional response, the central drivers of which are the hypoxia-inducible factor (HIF) family of transcription factors. HIFs are regulated in an oxygen-dependent manner and while their role in hypoxia is well established, it is apparent that other key players are required for gene expression control in hypoxia. In this review, we highlight the current understanding of the known and potential molecular mechanisms underpinning gene transcriptional responses to hypoxia in mammals, with a focus on oxygen-dependent effects on chromatin structure.
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15
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Kindrick JD, Mole DR. Hypoxic Regulation of Gene Transcription and Chromatin: Cause and Effect. Int J Mol Sci 2020; 21:E8320. [PMID: 33171917 PMCID: PMC7664190 DOI: 10.3390/ijms21218320] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 12/11/2022] Open
Abstract
Cellular responses to low oxygen (hypoxia) are fundamental to normal physiology and to the pathology of many common diseases. Hypoxia-inducible factor (HIF) is central to this by enhancing the transcriptional activity of many hundreds of genes. The cellular response to HIF is cell-type-specific and is largely governed by the pre-existing epigenetic landscape. Prior to activation, HIF-binding sites and the promoters of HIF-target genes are already accessible, in contact with each other through chromatin looping and display markers of activity. However, hypoxia also modulates the epigenetic environment, both in parallel to and as a consequence of HIF activation. This occurs through a combination of oxygen-sensitive changes in enzyme activity, transcriptional activation of epigenetic modifiers, and localized recruitment to chromatin by HIF and activated RNApol2. These hypoxic changes in the chromatin environment may both contribute to and occur as a consequence of transcriptional regulation. Nevertheless, they have the capacity to both modulate and extend the transcriptional response to hypoxia.
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Affiliation(s)
| | - David R. Mole
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FZ, UK;
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16
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Sun W, Li A, Wang Z, Sun X, Dong M, Qi F, Wang L, Zhang Y, Du P. Tetramethylpyrazine alleviates acute kidney injury by inhibiting NLRP3/HIF‑1α and apoptosis. Mol Med Rep 2020; 22:2655-2664. [PMID: 32945382 PMCID: PMC7453617 DOI: 10.3892/mmr.2020.11378] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
The aim of the present study was to investigate the protective effect and underlying mechanism of tetramethylpyrazine (TMP) on renal ischemia reperfusion injury (RIRI) in rats, which refers to the injury caused by the restoration of blood supply and reperfusion of the kidney after a period of ischemia. Sprague‑Dawley rats were randomly divided into a Sham group, renal ischemia‑reperfusion (I/R) group and TMP group. TMP hydrochloride (40 mg/kg, 6 h intervals) was given via intraperitoneal injection immediately after reperfusion in the TMP group, after 24 h the kidney tissues were taken for follow‑up experiments. Pathological changes in the kidney tissues were observed by periodic acid‑Schiff staining. Renal function was assessed by measuring levels of serum creatinine and blood urea nitrogen, and inflammatory cytokines tumor necrosis factor (TNF)‑α and interleukin (IL)‑6. Renal cell apoptosis was detected by TUNEL‑DAPI double staining, mRNA and protein changes were analyzed by reverse transcription‑quantitative PCR and western blotting. Cell viability was measured using a CCK‑8 assay. It was found that the renal tissues of the sham operation group were notably abnormal, and the renal tissues of the I/R group were damaged, while the renal tissues of the TMP group were less damaged compared with those of the I/R group. Compared with the I/R group, the serum creatinine and blood urea nitrogen levels in the TMP group were low (all P<0.05), levels of inflammatory cytokines TNF‑α and IL‑6 decreased, the apoptotic rate was low (all P<0.05), and the relative expression levels of nucleotide‑oligomerization domain‑like receptor 3 (NLRP3) protein and mRNA in renal tissues were low (all P<0.05). The expression levels of hypoxia‑inducible factor 1‑α and NLRP3 increased after oxygen and glucose deprivation (OGD), and reduced after treatment with OGD and TMP (all P<0.05). It was concluded that TMP can reduce renal injury and improve renal function in RIRI rats, and its mechanism may be related to the reduction of NLRP3 expression in renal tissues.
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Affiliation(s)
- Wangnan Sun
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Aiqun Li
- Emergency Department, Yantai Affiliated Hospital, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Zhiqiang Wang
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Xuhong Sun
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Menghua Dong
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Fu Qi
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Lin Wang
- Department of Geriatrics, the Second Hospital of Shandong University, Jinan, Shandong 264001, P.R. China
| | - Yueheng Zhang
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Pengchao Du
- Institute of Pathology and Pathophysiology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
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17
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Wilson JW, Shakir D, Batie M, Frost M, Rocha S. Oxygen-sensing mechanisms in cells. FEBS J 2020; 287:3888-3906. [PMID: 32446269 DOI: 10.1111/febs.15374] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022]
Abstract
The importance of oxygen for the survival of multicellular and aerobic organisms is well established and documented. Over the years, increased knowledge of its use for bioenergetics has placed oxygen at the centre of research on mitochondria and ATP-generating processes. Understanding the molecular mechanisms governing cellular oxygen sensing and response has allowed for the discovery of novel pathways oxygen is involved in, culminating with the award of the Nobel Prize for Medicine and Physiology in 2019 to the pioneers of this field, Greg Semenza, Peter Ratcliffe and William Kaelin. However, it is now beginning to be appreciated that oxygen can be a signalling molecule involved in a vast array of molecular processes, most of which impinge on gene expression control. This review will focus on the knowns and unknowns of oxygen as a signalling molecule, highlighting the role of 2-oxoglutarate-dependent dioxygenases as central players in the cellular response to deviations in oxygen tension.
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Affiliation(s)
- James W Wilson
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, UK
| | - Dilem Shakir
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, UK
| | - Michael Batie
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, UK
| | - Mark Frost
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, UK
| | - Sonia Rocha
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, UK
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18
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Kim I, Park JW. Hypoxia-driven epigenetic regulation in cancer progression: A focus on histone methylation and its modifying enzymes. Cancer Lett 2020; 489:41-49. [PMID: 32522693 DOI: 10.1016/j.canlet.2020.05.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/28/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
The mechanism underlying hypoxia-driven chromatin remodeling is a long-lasting question. For the last two decades, this question has been resolved in part. It is now widely agreed that hypoxia dynamically changes the methylation status of histones to control gene expression. Hypoxia-inducible factor (HIF) plays a central role in cellular responses to hypoxia through transcriptional activation of numerous genes. At least in part, the hypoxic regulation of histone methylation is attributed to the HIF-mediated expression of histone modifying enzymes. Protein hydroxylation and histone demethylation have emerged as the oxygen sensing processes because they are catalyzed by a family of 2-oxoglutarate (2OG)-dependent dioxygenases whose activities depend upon the ambient oxygen level. Recently, it has been extensively investigated that the 2OG dioxygenases oxygen-dependently regulate histone methylation. Nowadays, the hypoxic change in the histone methylation status is regarded as an important event to drive malignant behaviors of cancer cells. In this review, we introduced and summarized the cellular processes that govern hypoxia-driven regulation of histone methylation in the context of cancer biology. We also discussed the emerging roles of histone methyltransferases and demethylases in epigenetic response to hypoxia.
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Affiliation(s)
- Iljin Kim
- Department of Pharmacology, Cancer Research Institute, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Wan Park
- Department of Pharmacology, Cancer Research Institute, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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19
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Yang H, Li G, Han N, Zhang X, Cao Y, Cao Y, Fan Z. Secreted frizzled-related protein 2 promotes the osteo/odontogenic differentiation and paracrine potentials of stem cells from apical papilla under inflammation and hypoxia conditions. Cell Prolif 2019; 53:e12694. [PMID: 31568642 PMCID: PMC6985663 DOI: 10.1111/cpr.12694] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/31/2019] [Accepted: 08/17/2019] [Indexed: 12/15/2022] Open
Abstract
Objectives Mesenchymal stem cell (MSC)‐based dental tissue regeneration is a potential treatment method in future, while inflammation and hypoxia niche will affect MSC‐mediated tissue regeneration. In this research, we intended to investigate the influence and mechanism of secreted frizzled‐related protein 2(SFRP2) on MSC function under inflammation and hypoxia conditions. Material and methods Stem cells from apical papilla (SCAPs) were used in this study. The alkaline phosphatase (ALP) activity, Alizarin Red S staining, scratch‐simulated wound migration and transwell chemotaxis assay were used to evaluate the functions of SFRP2. The Western blot, real‐time RT‐PCR and ChIP assays were used to evaluate the mechanism of SFRP2. Results Under inflammation and hypoxia conditions, the over‐expression of SFRP2 could enhance the osteo/odontogenic differentiation ability. Mechanismly, SFRP2 inhibited canonical Wnt/β‐catenin signalling pathway and then inhibited the target genes of nuclear factor kappa B (NFkB) signalling pathway. Inflammation or hypoxia conditions could promote the expression of lysine demethylase 2A (KDM2A) and repress SFRP2 transcription through decreasing histone methylation in the SFRP2 promoter. Besides, proteomic analysis showed that SFRP2 promoted SCAPs to secret more functional cytokines, which improve the migration, chemotaxis and osteo/odontogenic ability of MSCs. Conclusions Our discoveries revealed that SFRP2 enhanced the osteo/odontogenic differentiation and paracrine potentials of SCAPs under hypoxia and inflammation conditions and provided a potential cytokine for promoting tissue regeneration in hypoxia and inflammatory niche.
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Affiliation(s)
- Haoqing Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Guoqing Li
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Nannan Han
- Department of Periodontology, Capital Medical University School of Stomatology, Beijing, China
| | - Xiuli Zhang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Periodontology, Capital Medical University School of Stomatology, Beijing, China
| | - Yangyang Cao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Yu Cao
- Department of General Dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
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20
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Vacík T, Lađinović D, Raška I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus 2019; 9:431-441. [PMID: 30059280 PMCID: PMC7000146 DOI: 10.1080/19491034.2018.1498707] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aberrant levels of histone modifications lead to chromatin malfunctioning and consequently to various developmental defects and human diseases. Therefore, the proteins bearing the ability to modify histones have been extensively studied and the molecular mechanisms of their action are now fairly well understood. However, little attention has been paid to naturally occurring alternative isoforms of chromatin modifying proteins and to their biological roles. In this review, we focus on mammalian KDM2A and KDM2B, the only two lysine demethylases whose genes have been described to produce also an alternative isoform lacking the N-terminal demethylase domain. These short KDM2A/B-SF isoforms arise through alternative promoter usage and seem to play important roles in development and disease. We hypothesise about the biological significance of these alternative isoforms, which might represent a more common evolutionarily conserved regulatory mechanism.
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Affiliation(s)
- Tomáš Vacík
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Dijana Lađinović
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Ivan Raška
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
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21
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Batie M, Frost J, Frost M, Wilson JW, Schofield P, Rocha S. Hypoxia induces rapid changes to histone methylation and reprograms chromatin. Science 2019; 363:1222-1226. [DOI: 10.1126/science.aau5870] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/05/2018] [Accepted: 01/24/2019] [Indexed: 12/22/2022]
Abstract
Oxygen is essential for the life of most multicellular organisms. Cells possess enzymes called molecular dioxygenases that depend on oxygen for activity. A subclass of molecular dioxygenases is the histone demethylase enzymes, which are characterized by the presence of a Jumanji-C (JmjC) domain. Hypoxia can alter chromatin, but whether this is a direct effect on JmjC-histone demethylases or due to other mechanisms is unknown. Here, we report that hypoxia induces a rapid and hypoxia-inducible factor–independent induction of histone methylation in a range of human cultured cells. Genomic locations of histone-3 lysine-4 trimethylation (H3K4me3) and H3K36me3 after a brief exposure of cultured cells to hypoxia predict the cell’s transcriptional response several hours later. We show that inactivation of one of the JmjC-containing enzymes, lysine demethylase 5A (KDM5A), mimics hypoxia-induced cellular responses. These results demonstrate that oxygen sensing by chromatin occurs via JmjC-histone demethylase inhibition.
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22
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McCann TS, Sobral LM, Self C, Hsieh J, Sechler M, Jedlicka P. Biology and targeting of the Jumonji-domain histone demethylase family in childhood neoplasia: a preclinical overview. Expert Opin Ther Targets 2019; 23:267-280. [PMID: 30759030 DOI: 10.1080/14728222.2019.1580692] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Epigenetic mechanisms of gene regulatory control play fundamental roles in developmental morphogenesis, and, as more recently appreciated, are heavily implicated in the onset and progression of neoplastic disease, including cancer. Many epigenetic mechanisms are therapeutically targetable, providing additional incentive for understanding of their contribution to cancer and other types of neoplasia. Areas covered: The Jumonji-domain histone demethylase (JHDM) family exemplifies many of the above traits. This review summarizes the current state of knowledge of the functions and pharmacologic targeting of JHDMs in cancer and other neoplastic processes, with an emphasis on diseases affecting the pediatric population. Expert opinion: To date, the JHDM family has largely been studied in the context of normal development and adult cancers. In contrast, comparatively few studies have addressed JHDM biology in cancer and other neoplastic diseases of childhood, especially solid (non-hematopoietic) neoplasms. Encouragingly, the few available examples support important roles for JHDMs in pediatric neoplasia, as well as potential roles for JHDM pharmacologic inhibition in disease management. Further investigations of JHDMs in cancer and other types of neoplasia of childhood can be expected to both enlighten disease biology and inform new approaches to improve disease outcomes.
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Affiliation(s)
- Tyler S McCann
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Lays M Sobral
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Chelsea Self
- b Department of Pediatrics , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Joseph Hsieh
- c Medical Scientist Training Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Marybeth Sechler
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,d Cancer Biology Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
| | - Paul Jedlicka
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,c Medical Scientist Training Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA.,d Cancer Biology Program , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
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23
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Luo W, Wang Y. Hypoxia Mediates Tumor Malignancy and Therapy Resistance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1136:1-18. [PMID: 31201713 DOI: 10.1007/978-3-030-12734-3_1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hypoxia is a hallmark of the tumor microenvironment and contributes to tumor malignant phenotypes. Hypoxia-inducible factor (HIF) is a master regulator of intratumoral hypoxia and controls hypoxia-mediated pathological processes in tumors, including angiogenesis, metabolic reprogramming, epigenetic reprogramming, immune evasion, pH homeostasis, cell migration/invasion, stem cell pluripotency, and therapy resistance. In this book chapter, we reviewed the causes and types of intratumoral hypoxia, hypoxia detection methods, and the oncogenic role of HIF in tumorigenesis and chemo- and radio-therapy resistance.
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Affiliation(s)
- Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Yingfei Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX, USA.
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24
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Biddlestone J, Batie M, Bandarra D, Munoz I, Rocha S. SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression. Biochem J 2018; 475:2073-2090. [PMID: 29784889 PMCID: PMC6024822 DOI: 10.1042/bcj20170945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/15/2018] [Accepted: 05/21/2018] [Indexed: 01/09/2023]
Abstract
The SIN3A-HDAC (histone deacetylase) complex is a master transcriptional repressor, required for development but often deregulated in disease. Here, we report that the recently identified new component of this complex, SINHCAF (SIN3A and HDAC-associated factor)/FAM60A (family of homology 60A), links the SIN3A-HDAC co-repressor complex function to the hypoxia response. We show that SINHCAF specifically represses HIF-2α mRNA and protein expression, via its interaction with the transcription factor SP1 (specificity protein 1) and recruitment of HDAC1 to the HIF-2α promoter. SINHCAF control over HIF-2α results in functional cellular changes in in vitro angiogenesis and viability. Our analysis reveals an unexpected link between SINHCAF and the regulation of the hypoxia response.
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Affiliation(s)
- John Biddlestone
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
- SCREDS Clinical Lecturer in Plastic and Reconstructive Surgery, Centre for Cell Engineering, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Michael Batie
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
- Department of Biochemistry, Institute for Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Daniel Bandarra
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Ivan Munoz
- MRC Protein Phosphorylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Sonia Rocha
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
- Department of Biochemistry, Institute for Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
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25
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Batie M, Del Peso L, Rocha S. Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms. Biomedicines 2018; 6:biomedicines6020047. [PMID: 29690561 PMCID: PMC6027312 DOI: 10.3390/biomedicines6020047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/26/2018] [Accepted: 04/19/2018] [Indexed: 12/20/2022] Open
Abstract
Hypoxia or reduced oxygen availability has been studied extensively for its ability to activate specific genes. Hypoxia-induced gene expression is mediated by the HIF transcription factors, but not exclusively so. Despite the extensive knowledge about how hypoxia activates genes, much less is known about how hypoxia promotes gene repression. In this review, we discuss the potential mechanisms underlying hypoxia-induced transcriptional repression responses. We highlight HIF-dependent and independent mechanisms as well as the potential roles of dioxygenases with functions at the nucleosome and DNA level. Lastly, we discuss recent evidence regarding the involvement of transcriptional repressor complexes in hypoxia.
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Affiliation(s)
- Michael Batie
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
| | - Luis Del Peso
- Department of Biochemistry, Institute of Biomedical Research, Autonomous Madrid University, Arturo Duperier, 4. 28029 Madrid, Spain.
| | - Sonia Rocha
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L697ZB, UK.
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26
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Nicolini A, Ferrari P, Diodati L, Carpi A. Recent Advances in Comprehending the Signaling Pathways Involved in the Progression of Breast Cancer. Int J Mol Sci 2017; 18:E2321. [PMID: 29099748 PMCID: PMC5713290 DOI: 10.3390/ijms18112321] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/11/2022] Open
Abstract
This review describes recent advances in the comprehension of signaling pathways involved in breast cancer progression. Calcium sensing receptor (CaSR), caveolae signaling, signaling referred to hypoxia-inducing factors and disturbances in the apoptotic machinery are related to more general biological mechanisms and are considered first. The others refer to signaling pathways of more specific biological mechanisms, namely the heparin/heparin-sulfate interactome, over-expression of miRNA-378a-5p, restriction of luminal and basal epithelial cells, fatty-acid synthesis, molecular pathways related to epithelial to mesenchimal transition (EMT), HER-2/neu gene amplification and protein expression, and the expression of other members of the epithelial growth factor receptor family. This progress in basic research is fundamental to foster the ongoing efforts that use the new genotyping technologies, and aim at defining new prognostic and predictive biomarkers for a better personalized management of breast cancer disease.
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Affiliation(s)
- Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy.
| | - Paola Ferrari
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy.
| | - Lucrezia Diodati
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy.
| | - Angelo Carpi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy.
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27
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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.
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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.
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