1
|
Ortiz GGR, Mohammadi Y, Nazari A, Ataeinaeini M, Kazemi P, Yasamineh S, Al-Naqeeb BZT, Zaidan HK, Gholizadeh O. A state-of-the-art review on the MicroRNAs roles in hematopoietic stem cell aging and longevity. Cell Commun Signal 2023; 21:85. [PMID: 37095512 PMCID: PMC10123996 DOI: 10.1186/s12964-023-01117-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/25/2023] [Indexed: 04/26/2023] Open
Abstract
Aging is a biological process determined through time-related cellular and functional impairments, leading to a decreased standard of living for the organism. Recently, there has been an unprecedented advance in the aging investigation, especially the detection that the rate of senescence is at least somewhat regulated via evolutionarily preserved genetic pathways and biological processes. Hematopoietic stem cells (HSCs) maintain blood generation over the whole lifetime of an organism. The senescence process influences many of the natural features of HSC, leading to a decline in their capabilities, independently of their microenvironment. New studies show that HSCs are sensitive to age-dependent stress and gradually lose their self-renewal and regeneration potential with senescence. MicroRNAs (miRNAs) are short, non-coding RNAs that post-transcriptionally inhibit translation or stimulate target mRNA cleavage of target transcripts via the sequence-particular connection. MiRNAs control various biological pathways and processes, such as senescence. Several miRNAs are differentially expressed in senescence, producing concern about their use as moderators of the senescence process. MiRNAs play an important role in the control of HSCs and can also modulate processes associated with tissue senescence in specific cell types. In this review, we display the contribution of age-dependent alterations, including DNA damage, epigenetic landscape, metabolism, and extrinsic factors, which affect HSCs function during aging. In addition, we investigate the particular miRNAs regulating HSCs senescence and age-associated diseases. Video Abstract.
Collapse
Affiliation(s)
- Geovanny Genaro Reivan Ortiz
- Laboratory of Basic Psychology, Behavioral Analysis and Programmatic Development (PAD-LAB), Catholic University of Cuenca, Cuenca, Ecuador
| | - Yasaman Mohammadi
- Faculty of Dentistry, Islamic Azad University, Shiraz Branch, Shiraz, Iran
| | - Ahmad Nazari
- Tehran University of Medical Sciences, Tehran, Iran
| | | | - Parisa Kazemi
- Faculty of Dentistry, Ilam University of Medical Sciences, Ilam, Iran
| | - Saman Yasamineh
- Stem Cell Research Center at, Tabriz University of Medical Sciences, Tabriz, Iran.
| | | | - Haider Kamil Zaidan
- Department of Medical Laboratories Techniques, Al-Mustaqbal University College, Hillah, Babylon, Iraq
| | - Omid Gholizadeh
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
2
|
Agrawal-Singh S, Bagri J, Giotopoulos G, Azazi DMA, Horton SJ, Lopez CK, Anand S, Bach AS, Stedham F, Antrobus R, Houghton JW, Vassiliou GS, Sasca D, Yun H, Whetton AD, Huntly BJP. HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia. Blood 2023; 141:1737-1754. [PMID: 36577137 PMCID: PMC10113176 DOI: 10.1182/blood.2022016528] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022] Open
Abstract
HOXA9 is commonly upregulated in acute myeloid leukemia (AML), in which it confers a poor prognosis. Characterizing the protein interactome of endogenous HOXA9 in human AML, we identified a chromatin complex of HOXA9 with the nuclear matrix attachment protein SAFB. SAFB perturbation phenocopied HOXA9 knockout to decrease AML proliferation, increase differentiation and apoptosis in vitro, and prolong survival in vivo. Integrated genomic, transcriptomic, and proteomic analyses further demonstrated that the HOXA9-SAFB (H9SB)-chromatin complex associates with nucleosome remodeling and histone deacetylase (NuRD) and HP1γ to repress the expression of factors associated with differentiation and apoptosis, including NOTCH1, CEBPδ, S100A8, and CDKN1A. Chemical or genetic perturbation of NuRD and HP1γ-associated catalytic activity also triggered differentiation, apoptosis, and the induction of these tumor-suppressive genes. Importantly, this mechanism is operative in other HOXA9-dependent AML genotypes. This mechanistic insight demonstrates the active HOXA9-dependent differentiation block as a potent mechanism of disease maintenance in AML that may be amenable to therapeutic intervention by targeting the H9SB interface and/or NuRD and HP1γ activity.
Collapse
Affiliation(s)
- Shuchi Agrawal-Singh
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Jaana Bagri
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - George Giotopoulos
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Dhoyazan M A Azazi
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Horton
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Cecile K Lopez
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Shubha Anand
- Cancer Molecular Diagnostics Laboratory, Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Anne-Sophie Bach
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Frances Stedham
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Jack W Houghton
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - George S Vassiliou
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Daniel Sasca
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - Haiyang Yun
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Anthony D Whetton
- School of Veterinary Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
3
|
Florentin J, Zhao J, Tai YY, Sun W, Ohayon LL, O'Neil SP, Arunkumar A, Zhang X, Zhu J, Al Aaraj Y, Watson A, Sembrat J, Rojas M, Chan SY, Dutta P. Loss of Amphiregulin drives inflammation and endothelial apoptosis in pulmonary hypertension. Life Sci Alliance 2022; 5:5/11/e202101264. [PMID: 35732465 PMCID: PMC9218345 DOI: 10.26508/lsa.202101264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 12/15/2022] Open
Abstract
Pulmonary hypertension (PH) is a vascular disease characterized by elevated pulmonary arterial pressure, leading to right ventricular failure and death. Pathogenic features of PH include endothelial apoptosis and vascular inflammation, which drive vascular remodeling and increased pulmonary arterial pressure. Re-analysis of the whole transcriptome sequencing comparing human pulmonary arterial endothelial cells (PAECs) isolated from PH and control patients identified AREG, which encodes Amphiregulin, as a key endothelial survival factor. PAECs from PH patients and mice exhibited down-regulation of AREG and its receptor epidermal growth factor receptor (EGFR). Moreover, the deficiency of AREG and EGFR in ECs in vivo and in vitro heightened inflammatory leukocyte recruitment, cytokine production, and endothelial apoptosis, as well as diminished angiogenesis. Correspondingly, hypoxic mice lacking Egfr in ECs (cdh5 cre/+ Egfr fl/fl) displayed elevated RVSP and pulmonary remodeling. Computational analysis identified NCOA6, PHB2, and RRP1B as putative genes regulating AREG in endothelial cells. The master transcription factor of hypoxia HIF-1⍺ binds to the promoter regions of these genes and up-regulates their expression in hypoxia. Silencing of these genes in cultured PAECs decreased inflammation and apoptosis, and increased angiogenesis in hypoxic conditions. Our pathway analysis and gene silencing experiments revealed that BCL2-associated agonist of cell death (BAD) is a downstream mediator of AREG BAD silencing in ECs lacking AREG mitigated inflammation and apoptosis, and suppressed tube formation. In conclusion, loss of Amphiregulin and its receptor EGFR in PH is a crucial step in the pathogenesis of PH, promoting pulmonary endothelial cell death, influx of inflammatory myeloid cells, and vascular remodeling.
Collapse
Affiliation(s)
- Jonathan Florentin
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jingsi Zhao
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yi-Yin Tai
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Wei Sun
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lee L Ohayon
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Scott P O'Neil
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Anagha Arunkumar
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xinyi Zhang
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jianhui Zhu
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yassmin Al Aaraj
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Annie Watson
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen Y Chan
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Partha Dutta
- Division of Cardiology, Department of Medicine, Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA .,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
4
|
Farooq U, Notani D. Transcriptional regulation of INK4/ARF locus by cis and trans mechanisms. Front Cell Dev Biol 2022; 10:948351. [PMID: 36158211 PMCID: PMC9500187 DOI: 10.3389/fcell.2022.948351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/09/2022] [Indexed: 12/12/2022] Open
Abstract
9p21 locus is one of the most reproducible regions in genome-wide association studies (GWAS). The region harbors CDKN2A/B genes that code for p16INK4a, p15INK4b, and p14ARF proteins, and it also harbors a long gene desert adjacent to these genes. The polymorphisms that are associated with several diseases and cancers are present in these genes and the gene desert region. These proteins are critical cell cycle regulators whose transcriptional dysregulation is strongly linked with cellular regeneration, stemness, aging, and cancers. Given the importance of this locus, intense scientific efforts on understanding the regulation of these genes via promoter-driven mechanisms and recently, via the distal regulatory mechanism have provided major insights. In this review, we describe these mechanisms and propose the ways by which this locus can be targeted in pathologies and aging.
Collapse
Affiliation(s)
- Umer Farooq
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
| | - Dimple Notani
- Genetics and Development, National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore, India
- *Correspondence: Umer Farooq, ; Dimple Notani,
| |
Collapse
|
5
|
A high-affinity cocaine binding site associated with the brain acid soluble protein 1. Proc Natl Acad Sci U S A 2022; 119:e2200545119. [PMID: 35412917 PMCID: PMC9169839 DOI: 10.1073/pnas.2200545119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cocaine is a monoamine transport inhibitor. Current models attributing pharmacologic actions of cocaine to inhibiting the activity of the amine transporters alone failed to translate to the clinic. Cocaine inhibition of the dopamine, serotonin, and norepinephrine transporters is relatively weak, suggesting that blockade of the amine transporters alone cannot account for the actions of cocaine, especially at low doses. There is evidence for significantly more potent actions of cocaine, suggesting the existence of a high-affinity receptor(s) for the drug. Identifying and characterizing such receptors will deepen our understanding of cocaine pharmacologic actions and pave the way for therapeutic development. Here we identify a high-affinity cocaine binding site associated with BASP1 that is involved in mediating the drug’s psychotropic actions. Cocaine exerts its stimulant effect by inhibiting dopamine (DA) reuptake, leading to increased dopamine signaling. This action is thought to reflect the binding of cocaine to the dopamine transporter (DAT) to inhibit its function. However, cocaine is a relatively weak inhibitor of DAT, and many DAT inhibitors do not share cocaine’s behavioral actions. Further, recent reports show more potent actions of the drug, implying the existence of a high-affinity receptor for cocaine. We now report high-affinity binding of cocaine associated with the brain acid soluble protein 1 (BASP1) with a dissociation constant (Kd) of 7 nM. Knocking down BASP1 in the striatum inhibits [3H]cocaine binding to striatal synaptosomes. Depleting BASP1 in the nucleus accumbens but not the dorsal striatum diminishes locomotor stimulation in mice. Our findings imply that BASP1 is a pharmacologically relevant receptor for cocaine.
Collapse
|
6
|
Aitken TJ, Crabtree JE, Jensen DM, Hess KH, Leininger BR, Tessem JS. Decreased proliferation of aged rat beta cells corresponds with enhanced expression of the cell cycle inhibitor p27 KIP1. Biol Cell 2021; 113:507-521. [PMID: 34523154 DOI: 10.1111/boc.202100035] [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] [Received: 05/18/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Over 400 million people are diabetic. Type 1 and type 2 diabetes are characterized by decreased functional β-cell mass and, consequently, decreased glucose-stimulated insulin secretion. A potential intervention is transplantation of β-cell containing islets from cadaveric donors. A major impediment to greater application of this treatment is the scarcity of transplant-ready β-cells. Therefore, inducing β-cell proliferation ex vivo could be used to expand functional β-cell mass prior to transplantation. Various molecular pathways are sufficient to induce proliferation of young β-cells; however, aged β-cells are refractory to these proliferative signals. Given that the majority of cadaveric donors fit an aged demographic, defining the mechanisms that impede aged β-cell proliferation is imperative. RESULTS We demonstrate that aged rat (5-month-old) β-cells are refractory to mitogenic stimuli that otherwise induce young rat (5-week-old) β-cell proliferation. We hypothesized that this change in proliferative capacity could be due to differences in cyclin-dependent kinase inhibitor expression. We measured levels of p16INK4a , p15INK4b , p18INK4c , p19INK4d , p21CIP1 , p27KIP1 and p57KIP2 by immunofluorescence analysis. Our data demonstrates an age-dependent increase of p27KIP1 in rat β-cells by immunofluorescence and was validated by increased p27KIP1 protein levels by western blot analysis. Interestingly, HDAC1, which modulates the p27KIP1 promoter acetylation state, is downregulated in aged rat islets. These data demonstrate increased p27KIP1 protein levels at 5 months of age, which may be due to decreased HDAC1 mediated repression of p27KIP1 expression. SIGNIFICANCE As the majority of transplant-ready β-cells come from aged donors, it is imperative that we understand why aged β-cells are refractory to mitogenic stimuli. Our findings demonstrate that increased p27KIP1 expression occurs early in β-cell aging, which corresponds with impaired β-cell proliferation. Furthermore, the correlation between HDAC1 and p27 levels suggests that pathways that activate HDAC1 in aged β-cells could be leveraged to decrease p27KIP1 levels and enhance β-cell proliferation.
Collapse
Affiliation(s)
- Talon J Aitken
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, Provo, Utah, USA.,Medical Education Program, Des Moines University, Des Moines, IA, 50312, USA
| | - Jacqueline E Crabtree
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, Provo, Utah, USA
| | - Daelin M Jensen
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, Provo, Utah, USA.,Biomedical Sciences, Ohio State University, Columbus, OH, 43210, USA
| | - Kavan H Hess
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, Provo, Utah, USA.,Medical Education Program, Idaho College of Osteopathic Medicine, Meridian, ID, 83642, USA
| | - Brennan R Leininger
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, Provo, Utah, USA.,Dental Education Program, UCLA School of Dentistry, Los Angeles, CA, 90024, USA
| | - Jeffery S Tessem
- Department of Nutrition, Dietetics, and Food Science, Brigham Young University, Provo, Utah, USA
| |
Collapse
|
7
|
Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
Collapse
|
8
|
Roupakia E, Markopoulos GS, Kolettas E. Genes and pathways involved in senescence bypass identified by functional genetic screens. Mech Ageing Dev 2021; 194:111432. [PMID: 33422562 DOI: 10.1016/j.mad.2021.111432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 10/22/2022]
Abstract
Cellular senescence is a state of stable and irreversible cell cycle arrest with active metabolism, that normal cells undergo after a finite number of divisions (Hayflick limit). Senescence can be triggered by intrinsic and/or extrinsic stimuli including telomere shortening at the end of a cell's lifespan (telomere-initiated senescence) and in response to oxidative, genotoxic or oncogenic stresses (stress-induced premature senescence). Several effector mechanisms have been proposed to explain senescence programmes in diploid cells, including the induction of DNA damage responses, a senescence-associated secretory phenotype and epigenetic changes. Senescent cells display senescence-associated-β-galactosidase activity and undergo chromatin remodeling resulting in heterochromatinisation. Senescence is established by the pRb and p53 tumour suppressor networks. Senescence has been detected in in vitro cellular settings and in premalignant, but not malignant lesions in mice and humans expressing mutant oncogenes. Despite oncogene-induced senescence, which is believed to be a cancer initiating barrier and other tumour suppressive mechanisms, benign cancers may still develop into malignancies by bypassing senescence. Here, we summarise the functional genetic screens that have identified genes, uncovered pathways and characterised mechanisms involved in senescence evasion. These include cell cycle regulators and tumour suppressor pathways, DNA damage response pathways, epigenetic regulators, SASP components and noncoding RNAs.
Collapse
Affiliation(s)
- Eugenia Roupakia
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece
| | - Georgios S Markopoulos
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece
| | - Evangelos Kolettas
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, Ioannina, 45100, Greece; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, 45110, Greece.
| |
Collapse
|
9
|
Abstract
Cellular senescence is a highly stable cell cycle arrest that is elicited in response to different stresses. By imposing a growth arrest, senescence limits the replication of old or damaged cells. Besides exiting the cell cycle, senescent cells undergo many other phenotypic alterations such as metabolic reprogramming, chromatin rearrangement, or autophagy modulation. In addition, senescent cells produce and secrete a complex combination of factors, collectively referred as the senescence-associated secretory phenotype, that mediate most of their non-cell-autonomous effects. Because senescent cells influence the outcome of a variety of physiological and pathological processes, including cancer and age-related diseases, pro-senescent and anti-senescent therapies are actively being explored. In this Review, we discuss the mechanisms regulating different aspects of the senescence phenotype and their functional implications. This knowledge is essential to improve the identification and characterization of senescent cells in vivo and will help to develop rational strategies to modulate the senescence program for therapeutic benefit.
Collapse
Affiliation(s)
- Nicolás Herranz
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jesús Gil
- MRC London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
10
|
Choi SW, Lee JY, Kang KS. miRNAs in stem cell aging and age-related disease. Mech Ageing Dev 2017; 168:20-29. [DOI: 10.1016/j.mad.2017.08.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 07/21/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
|
11
|
McHugh D, Gil J. Senescence and aging: Causes, consequences, and therapeutic avenues. J Cell Biol 2017; 217:65-77. [PMID: 29114066 PMCID: PMC5748990 DOI: 10.1083/jcb.201708092] [Citation(s) in RCA: 620] [Impact Index Per Article: 88.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/09/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Aging is the major risk factor for cancer, cardiovascular disease, diabetes, and neurodegenerative disorders. Although we are far from understanding the biological basis of aging, research suggests that targeting the aging process itself could ameliorate many age-related pathologies. Senescence is a cellular response characterized by a stable growth arrest and other phenotypic alterations that include a proinflammatory secretome. Senescence plays roles in normal development, maintains tissue homeostasis, and limits tumor progression. However, senescence has also been implicated as a major cause of age-related disease. In this regard, recent experimental evidence has shown that the genetic or pharmacological ablation of senescent cells extends life span and improves health span. Here, we review the cellular and molecular links between cellular senescence and aging and discuss the novel therapeutic avenues that this connection opens.
Collapse
Affiliation(s)
- Domhnall McHugh
- Medical Research Council London Institute of Medical Sciences, London, England, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, England, UK
| | - Jesús Gil
- Medical Research Council London Institute of Medical Sciences, London, England, UK .,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, England, UK
| |
Collapse
|
12
|
Abstract
PURPOSE OF REVIEW HOXA9 is a homeodomain transcription factor that plays an essential role in normal hematopoiesis and acute leukemia, in which its overexpression is strongly correlated with poor prognosis. The present review highlights recent advances in the understanding of genetic alterations leading to deregulation of HOXA9 and the downstream mechanisms of HOXA9-mediated transformation. RECENT FINDINGS A variety of genetic alterations including MLL translocations, NUP98-fusions, NPM1 mutations, CDX deregulation, and MOZ-fusions lead to high-level HOXA9 expression in acute leukemias. The mechanisms resulting in HOXA9 overexpression are beginning to be defined and represent attractive therapeutic targets. Small molecules targeting MLL-fusion protein complex members, such as DOT1L and menin, have shown promising results in animal models, and a DOT1L inhibitor is currently being tested in clinical trials. Essential HOXA9 cofactors and collaborators are also being identified, including transcription factors PU.1 and C/EBPα, which are required for HOXA9-driven leukemia. HOXA9 targets including IGF1, CDX4, INK4A/INK4B/ARF, mir-21, and mir-196b and many others provide another avenue for potential drug development. SUMMARY HOXA9 deregulation underlies a large subset of aggressive acute leukemias. Understanding the mechanisms regulating the expression and activity of HOXA9, along with its critical downstream targets, shows promise for the development of more selective and effective leukemia therapies.
Collapse
|
13
|
Abstract
Senescence contributes to the local and systemic aging of tissues and has been associated with age-related diseases. Recently, roles for this process during pregnancy have come to light, the dysregulation of which has been associated with adverse pregnancy outcomes such as preterm birth. Here, we summarize recent advances that support a role for senescence in birth timing and propose new aspects of study in this emerging field.
Collapse
Affiliation(s)
- Jeeyeon M Cha
- a Division of Diabetes, Endocrinology and Metabolism , Vanderbilt University Medical Center , Nashville , TN , USA.,b Department of Medicine , Vanderbilt University Medical Center , Nashville , TN , USA
| | - David M Aronoff
- b Department of Medicine , Vanderbilt University Medical Center , Nashville , TN , USA.,c Division of Infectious Diseases , Vanderbilt University Medical Center , Nashville , TN , USA.,d Department of Pathology, Microbiology and Immunology , Vanderbilt University Medical Center , Nashville , TN , USA
| |
Collapse
|
14
|
Downregulation of PARP1 transcription by promoter-associated E2F4-RBL2-HDAC1-BRM complex contributes to repression of pluripotency stem cell factors in human monocytes. Sci Rep 2017; 7:9483. [PMID: 28842672 PMCID: PMC5572705 DOI: 10.1038/s41598-017-10307-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/27/2017] [Indexed: 01/10/2023] Open
Abstract
Differentiation of certain cell types is followed by a downregulation of PARP1 expression. We show that the reduction in the abundance of PARP1 in hematopoietic progenitor cells and monocytes is tightly controlled by the cell cycle. The differentiation-associated cell cycle exit induces E2F1 replacement with E2F4 at the PARP1 promoter and the assembly of an E2F4-RBL2-HDAC1-BRM(SWI/SNF) repressor complex which deacetylates nucleosomes and compacts chromatin. In G1 arrested cells, PARP1 transcription is reduced by the recruitment of E2F1-RB1-HDAC1-EZH2(PRC2)-BRM/BRG1(SWI/SNF), which additionally trimethylates H3K27 and causes an even higher increase in nucleosome density. The re-establishment of an active chromatin structure by treating post-mitotic monocytes with the HDAC inhibitor and G1 arrested cells with a combination of HDAC and EZH2 inhibitors restores PARP1 expression completely but does not affect the interaction between the components of the repressor complex with chromatin. This suggests that RB1 and RBL2, as well as PRC2, SWI/SNF and HDAC1, do not interfere with the transcription machinery. Interestingly, reinstatement of PARP1 expression by the silencing of RBL2 or by the inhibition of HDACs in monocytes and by transfection with the PARP1 expression vector in differentiated THP-1 cells substantially increased transcription of pluripotency stem cell factors such as POU5F1, SOX2 and NANOG.
Collapse
|
15
|
Ni C, Narzt MS, Nagelreiter IM, Zhang CF, Larue L, Rossiter H, Grillari J, Tschachler E, Gruber F. Autophagy deficient melanocytes display a senescence associated secretory phenotype that includes oxidized lipid mediators. Int J Biochem Cell Biol 2016; 81:375-382. [PMID: 27732890 DOI: 10.1016/j.biocel.2016.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 01/06/2023]
Abstract
Autophagy is a recycling program which allows cells to adapt to metabolic needs and to stress. Defects in autophagy can affect metabolism, aging, proteostasis and inflammation. Autophagy pathway genes, including autophagy related 7 (Atg7), have been associated with the regulation of skin pigmentation, and autophagy defects disturb the biogenesis and transport of melanosomes in melanocytes as well as transfer and processing of melanin into keratinocytes. We have previously shown that mice whose melanocytes or keratinocytes lack Atg7 (and thus autophagy) as a result of specific gene knockout still retained functioning melanosome synthesis and transfer, and displayed only moderate reduction of pigmentation. In cell culture the Atg7 deficient melanocytes were prone to premature senescence and dysregulation of nuclear factor (erythroid-derived 2)-like 2 (Nrf2) signaling. To elucidate the biochemical basis of this phenotype, we performed a study on global gene expression, protein secretion and phospholipid composition in Atg7 deficient versus Atg7 expressing melanocytes. In cell culture Atg7 deficient melanocytes showed a pro-inflammatory gene expression signature and secreted higher levels of C-X-C motif chemokine ligand -1,-2,-10 and -12 (Cxcl1, Cxcl2, Cxcl10, Cxcl12), which are implicated in the pathogenesis of pigmentary disorders and expressed higher amounts of matrix metalloproteinases -3 and -13 (Mmp3, Mmp13). The analysis of membrane phospholipid composition identified an increase in the arachidonic- to linoleic acid ratio in the autophagy deficient cells, as well as an increase in oxidized phospholipid species that act as danger associated molecular patterns (DAMPs). The secretion of inflammation related factors suggests that autophagy deficient melanocytes display a senescence associated secretory phenotype (SASP), and we propose oxidized lipid mediators as novel components of this SASP.
Collapse
Affiliation(s)
- Chunya Ni
- Department of Dermatology, Medical University of Vienna, Währinger Grürtel 18-20, 1090 Vienna, Austria; Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Marie-Sophie Narzt
- Department of Dermatology, Medical University of Vienna, Währinger Grürtel 18-20, 1090 Vienna, Austria; Christian Doppler Laboratory for the Biotechnology of Skin Aging, Vienna, Austria
| | - Ionela-Mariana Nagelreiter
- Department of Dermatology, Medical University of Vienna, Währinger Grürtel 18-20, 1090 Vienna, Austria; Christian Doppler Laboratory for the Biotechnology of Skin Aging, Vienna, Austria
| | - Cheng Feng Zhang
- Department of Dermatology, Medical University of Vienna, Währinger Grürtel 18-20, 1090 Vienna, Austria; Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lionel Larue
- Institut Curie, Centre de Recherche, Developmental Genetics of Melanocytes, Orsay, France; CNRS UMR3347, Orsay, France; INSERM U1021, Orsay, France
| | - Heidemarie Rossiter
- Department of Dermatology, Medical University of Vienna, Währinger Grürtel 18-20, 1090 Vienna, Austria
| | - Johannes Grillari
- Christian Doppler Laboratory for the Biotechnology of Skin Aging, Vienna, Austria; Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, Währinger Grürtel 18-20, 1090 Vienna, Austria
| | - Florian Gruber
- Department of Dermatology, Medical University of Vienna, Währinger Grürtel 18-20, 1090 Vienna, Austria; Christian Doppler Laboratory for the Biotechnology of Skin Aging, Vienna, Austria.
| |
Collapse
|
16
|
Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements. PLoS Genet 2016; 12:e1006200. [PMID: 27466807 PMCID: PMC4965088 DOI: 10.1371/journal.pgen.1006200] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 06/25/2016] [Indexed: 12/24/2022] Open
Abstract
Polycomb group response elements (PREs) in Drosophila are DNA-elements that recruit Polycomb proteins (PcG) to chromatin and regulate gene expression. PREs are easily recognizable in the Drosophila genome as strong peaks of PcG-protein binding over discrete DNA fragments; many small but statistically significant PcG peaks are also observed in PcG domains. Surprisingly, in vivo deletion of the four characterized strong PREs from the PcG regulated invected-engrailed (inv-en) gene complex did not disrupt the formation of the H3K27me3 domain and did not affect inv-en expression in embryos or larvae suggesting the presence of redundant PcG recruitment mechanism. Further, the 3D-structure of the inv-en domain was only minimally altered by the deletion of the strong PREs. A reporter construct containing a 7.5kb en fragment that contains three weak peaks but no large PcG peaks forms an H3K27me3 domain and is PcG-regulated. Our data suggests a model for the recruitment of PcG-complexes to Drosophila genes via interactions with multiple, weak PREs spread throughout an H3K27me3 domain.
Collapse
|
17
|
Nelson DM, Jaber-Hijazi F, Cole JJ, Robertson NA, Pawlikowski JS, Norris KT, Criscione SW, Pchelintsev NA, Piscitello D, Stong N, Rai TS, McBryan T, Otte GL, Nixon C, Clark W, Riethman H, Wu H, Schotta G, Garcia BA, Neretti N, Baird DM, Berger SL, Adams PD. Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biol 2016; 17:158. [PMID: 27457071 PMCID: PMC4960804 DOI: 10.1186/s13059-016-1017-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/05/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Histone modification H4K20me3 and its methyltransferase SUV420H2 have been implicated in suppression of tumorigenesis. The underlying mechanism is unclear, although H4K20me3 abundance increases during cellular senescence, a stable proliferation arrest and tumor suppressor process, triggered by diverse molecular cues, including activated oncogenes. Here, we investigate the function of H4K20me3 in senescence and tumor suppression. RESULTS Using immunofluorescence and ChIP-seq we determine the distribution of H4K20me3 in proliferating and senescent human cells. Altered H4K20me3 in senescence is coupled to H4K16ac and DNA methylation changes in senescence. In senescent cells, H4K20me3 is especially enriched at DNA sequences contained within specialized domains of senescence-associated heterochromatin foci (SAHF), as well as specific families of non-genic and genic repeats. Altered H4K20me3 does not correlate strongly with changes in gene expression between proliferating and senescent cells; however, in senescent cells, but not proliferating cells, H4K20me3 enrichment at gene bodies correlates inversely with gene expression, reflecting de novo accumulation of H4K20me3 at repressed genes in senescent cells, including at genes also repressed in proliferating cells. Although elevated SUV420H2 upregulates H4K20me3, this does not accelerate senescence of primary human cells. However, elevated SUV420H2/H4K20me3 reinforces oncogene-induced senescence-associated proliferation arrest and slows tumorigenesis in vivo. CONCLUSIONS These results corroborate a role for chromatin in underpinning the senescence phenotype but do not support a major role for H4K20me3 in initiation of senescence. Rather, we speculate that H4K20me3 plays a role in heterochromatinization and stabilization of the epigenome and genome of pre-malignant, oncogene-expressing senescent cells, thereby suppressing epigenetic and genetic instability and contributing to long-term senescence-mediated tumor suppression.
Collapse
Affiliation(s)
- David M. Nelson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Farah Jaber-Hijazi
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - John J. Cole
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Neil A. Robertson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Jeffrey S. Pawlikowski
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Kevin T. Norris
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Steven W. Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903 USA
| | - Nikolay A. Pchelintsev
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Desiree Piscitello
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | | | - Taranjit Singh Rai
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
- Institute of Biomedical and Environmental Health Research, University of the West of Scotland, Paisley, PA1 2BE UK
| | - Tony McBryan
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - Gabriel L. Otte
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Colin Nixon
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | - William Clark
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| | | | - Hong Wu
- Fox Chase Cancer Center, Philadelphia, PA 19111 USA
| | - Gunnar Schotta
- Ludwig Maximilians University and Munich Center for Integrated Protein Science (CiPSM), Biomedical Center, Planegg-Martinsried, Germany
| | - Benjamin A. Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903 USA
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN UK
| | - Shelley L. Berger
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Peter D. Adams
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD UK
- Beatson Institute for Cancer Research, Glasgow, G61 1BD UK
| |
Collapse
|
18
|
Shields BJ, Jackson JT, Metcalf D, Shi W, Huang Q, Garnham AL, Glaser SP, Beck D, Pimanda JE, Bogue CW, Smyth GK, Alexander WS, McCormack MP. Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a. Genes Dev 2016; 30:78-91. [PMID: 26728554 PMCID: PMC4701980 DOI: 10.1101/gad.268425.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Here, Shields et al. demonstrate that the hematopoietically expressed homeobox gene Hhex is overexpressed in acute myeloid leukemia (AML) and is essential for the initiation and propagation of MLL-ENL-induced AML but dispensable for normal myelopoiesis, indicating a specific requirement for Hhex for leukemic growth. The findings in this study describe for the first time a nonclustered homeobox transcription factor that is essential for AML initiation and maintenance and provide mechanistic insight into these processes. Unlike clustered HOX genes, the role of nonclustered homeobox gene family members in hematopoiesis and leukemogenesis has not been extensively studied. Here we found that the hematopoietically expressed homeobox gene Hhex is overexpressed in acute myeloid leukemia (AML) and is essential for the initiation and propagation of MLL-ENL-induced AML but dispensable for normal myelopoiesis, indicating a specific requirement for Hhex for leukemic growth. Loss of Hhex leads to expression of the Cdkn2a-encoded tumor suppressors p16INK4a and p19ARF, which are required for growth arrest and myeloid differentiation following Hhex deletion. Mechanistically, we show that Hhex binds to the Cdkn2a locus and directly interacts with the Polycomb-repressive complex 2 (PRC2) to enable H3K27me3-mediated epigenetic repression. Thus, Hhex is a potential therapeutic target that is specifically required for AML stem cells to repress tumor suppressor pathways and enable continued self-renewal.
Collapse
Affiliation(s)
- Benjamin J Shields
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Jacob T Jackson
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Donald Metcalf
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia; Computing and Information Systems, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Qiutong Huang
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Alexandra L Garnham
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Stefan P Glaser
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Dominik Beck
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - John E Pimanda
- Lowy Cancer Research Centre and the Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Clifford W Bogue
- Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Gordon K Smyth
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia; Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Warren S Alexander
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Matthew P McCormack
- Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| |
Collapse
|
19
|
Liu T, Chen J, Xiao S, Lei X. H2.0-like homeobox 1 acts as a tumor suppressor in hepatocellular carcinoma. Tumour Biol 2015; 37:6419-28. [PMID: 26631039 DOI: 10.1007/s13277-015-4490-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 11/23/2015] [Indexed: 01/27/2023] Open
Abstract
H2.0-like homeobox 1 (HLX1) is a homeobox transcription factor gene expressed primarily in cytotrophoblast cell types in the early pregnancy human placenta and involved in the development of enteric nervous system. However, the biological function of HLX1 in hepatocellular carcinoma (HCC) remains unclear. In the present study, semiquantitative reverse transcription-polymerase chain reaction (RT-PCR), quantitative real-time RT-PCR, western blot, and immunohistochemical staining were used to examine the expression level of HLX1 in a total of 125 cases of HCC tissues and their matched adjacent nontumorous tissues (ANLTs), and its correlation with clinical features of HCC patients was analyzed. Our findings showed that the expression level of HLX1 was significantly reduced in HCCs compared to ANLTs. Besides, it was also remarkably downregulated in HCC cell lines compared to normal liver cell line. We further found that the HLX1 level was significantly associated with the tumor size (p = 0.016), tumor number (p = 0.004), vascular invasion (p = 0.031), Edmondson-Steiner grade (p = 0.041), tumor-node-metastasis (TNM) stage (p < 0.001), and Barcelona clinic liver cancer (BCLC) stage (p = 0.008). Moreover, HLX1 was an independent risk factor for overall survival (OS, p = 0.020) and disease-free survival (DFS, p = 0.024) of HCC patients. In vitro experiments showed that overexpression of HLX1 markedly suppressed the invasion, migration, proliferation, and colony formation of HCC cells; in contrast, downregulation of HLX1 significantly promoted the invasion, migration, proliferation, and colony formation of HCC cells. In vivo study indicated that overexpression of HLX1 significantly inhibited the tumorigenic capacity of HCC cells in nude mice. Based on these findings, we suggest that HLX1 acts as a tumor suppressor in HCC.
Collapse
Affiliation(s)
- Ting Liu
- Department of General Surgery, Second Xiangya Hospital, Central South University, Renmin Middle Road 139, Changsha, 410011, Hunan, China.
| | - Jing Chen
- Department of General Surgery, Peace Hospital Changzhi Medical College, Changzhi, 046000, Shanxi, China
| | - Shuai Xiao
- Department of General Surgery, Second Xiangya Hospital, Central South University, Renmin Middle Road 139, Changsha, 410011, Hunan, China
| | - Xiong Lei
- Department of Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| |
Collapse
|
20
|
Esposito MT, Zhao L, Fung TK, Rane JK, Wilson A, Martin N, Gil J, Leung AY, Ashworth A, So CWE. Synthetic lethal targeting of oncogenic transcription factors in acute leukemia by PARP inhibitors. Nat Med 2015; 21:1481-90. [PMID: 26594843 DOI: 10.1038/nm.3993] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 10/14/2015] [Indexed: 12/13/2022]
Abstract
Acute myeloid leukemia (AML) is mostly driven by oncogenic transcription factors, which have been classically viewed as intractable targets using small-molecule inhibitor approaches. Here we demonstrate that AML driven by repressive transcription factors, including AML1-ETO (encoded by the fusion oncogene RUNX1-RUNX1T1) and PML-RARα fusion oncoproteins (encoded by PML-RARA) are extremely sensitive to poly (ADP-ribose) polymerase (PARP) inhibition, in part owing to their suppressed expression of key homologous recombination (HR)-associated genes and their compromised DNA-damage response (DDR). In contrast, leukemia driven by mixed-lineage leukemia (MLL, encoded by KMT2A) fusions with dominant transactivation ability is proficient in DDR and insensitive to PARP inhibition. Intriguingly, genetic or pharmacological inhibition of an MLL downstream target, HOXA9, which activates expression of various HR-associated genes, impairs DDR and sensitizes MLL leukemia to PARP inhibitors (PARPis). Conversely, HOXA9 overexpression confers PARPi resistance to AML1-ETO and PML-RARα transformed cells. Together, these studies describe a potential utility of PARPi-induced synthetic lethality for leukemia treatment and reveal a novel molecular mechanism governing PARPi sensitivity in AML.
Collapse
MESH Headings
- Animals
- Apoptosis/drug effects
- Cell Differentiation/drug effects
- Cell Line, Transformed
- Cell Line, Tumor
- Cell Survival/drug effects
- Cellular Senescence/drug effects
- Core Binding Factor Alpha 2 Subunit/metabolism
- DNA Damage
- DNA Repair/drug effects
- Fluorescent Antibody Technique
- Gene Expression Regulation, Leukemic
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Oncogene Proteins, Fusion/metabolism
- Oncogenes
- Phthalazines/pharmacology
- Phthalazines/therapeutic use
- Piperazines/pharmacology
- Piperazines/therapeutic use
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use
- Poly(ADP-ribose) Polymerases/metabolism
- Protein Kinase Inhibitors/pharmacology
- RUNX1 Translocation Partner 1 Protein
- Transcription Factors/metabolism
Collapse
Affiliation(s)
- Maria Teresa Esposito
- Leukemia and Stem Cell Biology Group, Department of Haematological Medicine, Division of Cancer Studies, King's College London, London, UK
| | - Lu Zhao
- Leukemia and Stem Cell Biology Group, Department of Haematological Medicine, Division of Cancer Studies, King's College London, London, UK
| | - Tsz Kan Fung
- Leukemia and Stem Cell Biology Group, Department of Haematological Medicine, Division of Cancer Studies, King's College London, London, UK
| | - Jayant K Rane
- Leukemia and Stem Cell Biology Group, Department of Haematological Medicine, Division of Cancer Studies, King's College London, London, UK
| | - Amanda Wilson
- Leukemia and Stem Cell Biology Group, Department of Haematological Medicine, Division of Cancer Studies, King's College London, London, UK
| | - Nadine Martin
- Cell Proliferation Group, Medical Research Council Clinical Sciences Centre, Imperial College London, London, UK
| | - Jesus Gil
- Cell Proliferation Group, Medical Research Council Clinical Sciences Centre, Imperial College London, London, UK
| | - Anskar Y Leung
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alan Ashworth
- University of California, San Francisco (UCSF) Helen Diller Family Comprehensive Cancer Center, San Francisco, California, USA
| | - Chi Wai Eric So
- Leukemia and Stem Cell Biology Group, Department of Haematological Medicine, Division of Cancer Studies, King's College London, London, UK
| |
Collapse
|
21
|
Adrados I, Larrasa-Alonso J, Galarreta A, López-Antona I, Menéndez C, Abad M, Gil J, Moreno-Bueno G, Palmero I. The homeoprotein SIX1 controls cellular senescence through the regulation of p16INK4A and differentiation-related genes. Oncogene 2015; 35:3485-94. [PMID: 26500063 DOI: 10.1038/onc.2015.408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/04/2015] [Accepted: 09/18/2015] [Indexed: 12/13/2022]
Abstract
Cellular senescence is an antiproliferative response with essential functions in tumor suppression and tissue homeostasis. Here we show that SIX1, a member of the SIX family of homeobox transcriptional factors, is a novel repressor of senescence. Our data show that SIX1 is specifically downregulated in fibroblasts upon oncogenic stress and other pro-senescence stimuli, as well as in senescent skin premalignant lesions. Silencing of SIX1 in human fibroblasts suffices to trigger senescence, which is mediated by p16INK4A and lacks a canonical senescence-associated secretory phenotype. Interestingly, SIX1-associated senescence is further characterized by the expression of a set of development and differentiation-related genes that significantly overlap with genes associated with SIX1 in organogenesis or human tumors, and show coincident regulation in oncogene-induced senescence. Mechanistically, we show that gene regulation by SIX1 during senescence is mediated, at least in part, by cooperation with Polycomb repressive complexes. In summary, our results identify SIX1, a key development regulator altered in human tumors, as a critical repressor of cellular senescence, providing a novel connection between senescence, differentiation and tumorigenesis.
Collapse
Affiliation(s)
- I Adrados
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - J Larrasa-Alonso
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - A Galarreta
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - I López-Antona
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - C Menéndez
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - M Abad
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - J Gil
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London, UK
| | - G Moreno-Bueno
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain.,Departamento de Bioquímica, UAM, IdiPAZ (Instituto de Investigación Sanitaria La Paz) and Fundación MD Anderson Internacional, Madrid, Spain
| | - I Palmero
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| |
Collapse
|
22
|
Skvarova Kramarzova K, Fiser K, Mejstrikova E, Rejlova K, Zaliova M, Fornerod M, Drabkin HA, van den Heuvel-Eibrink MM, Stary J, Trka J, Starkova J. Homeobox gene expression in acute myeloid leukemia is linked to typical underlying molecular aberrations. J Hematol Oncol 2014; 7:94. [PMID: 25539595 PMCID: PMC4310032 DOI: 10.1186/s13045-014-0094-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/04/2014] [Indexed: 02/02/2023] Open
Abstract
Background Although distinct patterns of homeobox (HOX) gene expression have been described in defined cytogenetic and molecular subsets of patients with acute myeloid leukemia (AML), it is unknown whether these patterns are the direct result of transcriptional alterations or rather represent the differentiation stage of the leukemic cell. Method To address this question, we used qPCR to analyze mRNA expression of HOXA and HOXB genes in bone marrow (BM) samples of 46 patients with AML and sorted subpopulations of healthy BM cells. These various stages of myeloid differentiation represent matched counterparts of morphological subgroups of AML. To further study the transcriptional alterations of HOX genes in hematopoiesis, we also analyzed gene expression of epigenetic modifiers in the subpopluations of healthy BM and leukemic cells. Results Unsupervised hierarchical clustering divided the AMLs into five clusters characterized by the presence of prevalent molecular genetic aberrations. Notably, the impact of genotype on HOX gene expression was significantly more pronounced than that of the differentiation stage of the blasts. This driving role of molecular aberrations was best exemplified by the repressive effect of the PML-RARa fusion gene on HOX gene expression, regardless of the presence of the FLT3/ITD mutation. Furthermore, HOX gene expression was positively correlated with mRNA levels of histone demethylases (JMJD3 and UTX) and negatively correlated with gene expression of DNA methyltranferases. No such relationships were observed in subpopulations of healthy BM cells. Conclusion Our results demonstrate that specific molecular genetic aberrations, rather than differentiation per se, underlie the observed differences in HOX gene expression in AML. Moreover, the observed correlations between epigenetic modifiers and HOX ex pression that are specific to malignant hematopoiesis, suggest their potential causal relationships. Electronic supplementary material The online version of this article (doi:10.1186/s13045-014-0094-0) contains supplementary material, which is available to authorized users.
Collapse
|
23
|
Rai TS, Cole JJ, Nelson DM, Dikovskaya D, Faller WJ, Vizioli MG, Hewitt RN, Anannya O, McBryan T, Manoharan I, van Tuyn J, Morrice N, Pchelintsev NA, Ivanov A, Brock C, Drotar ME, Nixon C, Clark W, Sansom OJ, Anderson KI, King A, Blyth K, Adams PD. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes Dev 2014; 28:2712-25. [PMID: 25512559 PMCID: PMC4265675 DOI: 10.1101/gad.247528.114] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 11/04/2014] [Indexed: 01/06/2023]
Abstract
Cellular senescence is a stable proliferation arrest that suppresses tumorigenesis. Cellular senescence and associated tumor suppression depend on control of chromatin. Histone chaperone HIRA deposits variant histone H3.3 and histone H4 into chromatin in a DNA replication-independent manner. Appropriately for a DNA replication-independent chaperone, HIRA is involved in control of chromatin in nonproliferating senescent cells, although its role is poorly defined. Here, we show that nonproliferating senescent cells express and incorporate histone H3.3 and other canonical core histones into a dynamic chromatin landscape. Expression of canonical histones is linked to alternative mRNA splicing to eliminate signals that confer mRNA instability in nonproliferating cells. Deposition of newly synthesized histones H3.3 and H4 into chromatin of senescent cells depends on HIRA. HIRA and newly deposited H3.3 colocalize at promoters of expressed genes, partially redistributing between proliferating and senescent cells to parallel changes in expression. In senescent cells, but not proliferating cells, promoters of active genes are exceptionally enriched in H4K16ac, and HIRA is required for retention of H4K16ac. HIRA is also required for retention of H4K16ac in vivo and suppression of oncogene-induced neoplasia. These results show that HIRA controls a specialized, dynamic H4K16ac-decorated chromatin landscape in senescent cells and enforces tumor suppression.
Collapse
Affiliation(s)
- Taranjit Singh Rai
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom; Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, United Kingdom
| | - John J Cole
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - David M Nelson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Dina Dikovskaya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - William J Faller
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Maria Grazia Vizioli
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Rachael N Hewitt
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Orchi Anannya
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Tony McBryan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Indrani Manoharan
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - John van Tuyn
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Nicholas Morrice
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Nikolay A Pchelintsev
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Andre Ivanov
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Claire Brock
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Mark E Drotar
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom
| | - Colin Nixon
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - William Clark
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Owen J Sansom
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Kurt I Anderson
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Ayala King
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Karen Blyth
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom
| | - Peter D Adams
- Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, United Kingdom; Institute of Cancer Sciences, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G61 1BD, United Kingdom;
| |
Collapse
|
24
|
Martin N, Beach D, Gil J. Ageing as developmental decay: insights from p16INK4a. Trends Mol Med 2014; 20:667-74. [DOI: 10.1016/j.molmed.2014.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/07/2014] [Accepted: 09/09/2014] [Indexed: 01/03/2023]
|
25
|
Olivera-Martinez I, Schurch N, Li RA, Song J, Halley PA, Das RM, Burt DW, Barton GJ, Storey KG. Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo. Development 2014; 141:3266-76. [PMID: 25063452 PMCID: PMC4197544 DOI: 10.1242/dev.112623] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Here, we exploit the spatial separation of temporal events of neural differentiation in the elongating chick body axis to provide the first analysis of transcriptome change in progressively more differentiated neural cell populations in vivo. Microarray data, validated against direct RNA sequencing, identified: (1) a gene cohort characteristic of the multi-potent stem zone epiblast, which contains neuro-mesodermal progenitors that progressively generate the spinal cord; (2) a major transcriptome re-organisation as cells then adopt a neural fate; and (3) increasing diversity as neural patterning and neuron production begin. Focussing on the transition from multi-potent to neural state cells, we capture changes in major signalling pathways, uncover novel Wnt and Notch signalling dynamics, and implicate new pathways (mevalonate pathway/steroid biogenesis and TGFβ). This analysis further predicts changes in cellular processes, cell cycle, RNA-processing and protein turnover as cells acquire neural fate. We show that these changes are conserved across species and provide biological evidence for reduced proteasome efficiency and a novel lengthening of S phase. This latter step may provide time for epigenetic events to mediate large-scale transcriptome re-organisation; consistent with this, we uncover simultaneous downregulation of major chromatin modifiers as the neural programme is established. We further demonstrate that transcription of one such gene, HDAC1, is dependent on FGF signalling, making a novel link between signals that control neural differentiation and transcription of a core regulator of chromatin organisation. Our work implicates new signalling pathways and dynamics, cellular processes and epigenetic modifiers in neural differentiation in vivo, identifying multiple new potential cellular and molecular mechanisms that direct differentiation.
Collapse
Affiliation(s)
- Isabel Olivera-Martinez
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Nick Schurch
- Division of Computational Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Roman A Li
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Junfang Song
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Pamela A Halley
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Raman M Das
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dave W Burt
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Geoffrey J Barton
- Division of Computational Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Kate G Storey
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| |
Collapse
|
26
|
Gil J, O'Loghlen A. PRC1 complex diversity: where is it taking us? Trends Cell Biol 2014; 24:632-41. [PMID: 25065329 DOI: 10.1016/j.tcb.2014.06.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/16/2014] [Accepted: 06/24/2014] [Indexed: 12/22/2022]
Abstract
Polycomb group proteins (PcGs) are essential epigenetic regulators that play key roles in development, pluripotency, senescence, and cancer. Recent reports have found that the composition of mammalian Polycomb repressive complex 1 (PRC1) is far more varied than previously thought. PRC1 diversity largely depends on the presence of CBX proteins, dividing them into canonical and non-canonical, the existence of redundant subunits, and different binding affinities and/or regulation. However, there is no clear insight into how many functional PRC1 complexes exist and what the biological relevance is for such diversification. In this review we focus on mammalian PRC1 and discuss the mechanisms by which canonical and non-canonical PRC1 are recruited to chromatin, their role in normal development and disease, and emerging evidence for PRC1 as a transcriptional activator.
Collapse
Affiliation(s)
- Jesús Gil
- Cell Proliferation Group, Medical Research Council Clinical Sciences Centre, Imperial College London, Hammersmith Campus, London W12 0NN, UK
| | - Ana O'Loghlen
- Epigenetics and Cellular Senescence Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
| |
Collapse
|
27
|
Ueda K, Yoshimi A, Kagoya Y, Nishikawa S, Marquez VE, Nakagawa M, Kurokawa M. Inhibition of histone methyltransferase EZH2 depletes leukemia stem cell of mixed lineage leukemia fusion leukemia through upregulation of p16. Cancer Sci 2014; 105:512-9. [PMID: 24612037 PMCID: PMC4317832 DOI: 10.1111/cas.12386] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/19/2014] [Accepted: 02/20/2014] [Indexed: 12/25/2022] Open
Abstract
Leukemia stem cells (LSC) are resistant to conventional chemotherapy and persistent LSC after chemotherapy are supposed to be a major cause of relapse. However, information on genetic or epigenetic regulation of stem cell properties is still limited and LSC-targeted drugs have scarcely been identified. Epigenetic regulators are associated with many cellular processes including maintenance of stem cells. Of note are polycomb group proteins, because they potentially control stemness, and can be pharmacologically targeted by a selective inhibitor (DZNep). Therefore, we investigated the therapeutic potential of EZH2 inhibition in mixed lineage leukemia (MLL) fusion leukemia. Intriguingly, EZH2 inhibition by DZNep or shRNA not only suppressed MLL fusion leukemia proliferation but also reduced leukemia initiating cells (LIC) frequency. Expression analysis suggested that p16 upregulation was responsible for LICs reduction. Knockdown of p16 canceled the survival advantage of mice treated with DZNep. Chromatin immunoprecipitation assays demonstrated that EZH2 was highly enriched around the transcription-start-site of p16, together with H3K27 methylation marks in MLL/ENL and Hoxa9/Meis1 transduced cells but not in E2A/HLF transduced cells. Although high expression of Hoxa9 in MLL fusion leukemia is supposed to be responsible for the recruitment of EZH2, our data also suggest that there may be some other mechanisms independent of Hoxa9 activation to suppress p16 expression, because expression levels of Hoxa9 and p16 were not inversely related between MLL/ENL and Hoxa9/Meis1 transduced cells. In summary, our findings show that EZH2 is a potential therapeutic target of MLL fusion leukemia stem cells.
Collapse
Affiliation(s)
- Koki Ueda
- Department of Hematology and Oncology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | | |
Collapse
|
28
|
Serra RW, Fang M, Park SM, Hutchinson L, Green MR. A KRAS-directed transcriptional silencing pathway that mediates the CpG island methylator phenotype. eLife 2014; 3:e02313. [PMID: 24623306 PMCID: PMC3949416 DOI: 10.7554/elife.02313] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Approximately 70% of KRAS-positive colorectal cancers (CRCs) have a CpG island methylator phenotype (CIMP) characterized by aberrant DNA hypermethylation and transcriptional silencing of many genes. The factors involved in, and the mechanistic basis of, CIMP is not understood. Among the CIMP genes are the tumor suppressors p14ARF, p15INK4B, and p16INK4A, encoded by the INK4-ARF locus. In this study, we perform an RNA interference screen and identify ZNF304, a zinc-finger DNA-binding protein, as the pivotal factor required for INK4-ARF silencing and CIMP in CRCs containing activated KRAS. In KRAS-positive human CRC cell lines and tumors, ZNF304 is bound at the promoters of INK4-ARF and other CIMP genes. Promoter-bound ZNF304 recruits a corepressor complex that includes the DNA methyltransferase DNMT1, resulting in DNA hypermethylation and transcriptional silencing. KRAS promotes silencing through upregulation of ZNF304, which drives DNA binding. Finally, we show that ZNF304 also directs transcriptional silencing of INK4-ARF in human embryonic stem cells. DOI:http://dx.doi.org/10.7554/eLife.02313.001 Colorectal cancer, which affects the large intestine, is a leading cause of cancer deaths worldwide, ranking fourth after cancers of the lung, stomach, and liver. Like these other cancers, this disease is caused by mutations to genes that allow cells to multiply in an out of control manner. Mutations that change the gene encoding a protein called KRAS are found in many different types of cancer. Moreover, about 70% of colorectal cancers with a KRAS mutation also have an excess of small chemical marks on other genes, some of which are known to suppress the growth of tumors. These marks ‘switch off’ these genes, and although the identities of the enzymes that typically leave these marks on DNA are known, the link between these enzymes and the KRAS protein is unknown. Now Serra, Fang et al. have identified a protein, called ZNF304, that is required by KRAS to switch off a large number of genes, including multiple tumor suppressors. In the absence of ZNF304, these tumor suppressor genes remained switched on in cancer cells with the KRAS mutation, so the growth of the tumor was slowed down. ZNF304 is a protein that binds to stretches of DNA, including regions of DNA at the start of several tumor suppressor genes, and it recruits the enzymes that add the chemical marks that switch off these genes. Serra, Fang et al. found that the levels of ZNF304 protein were elevated in colorectal cancer cells with the mutated KRAS, and showed that this was due to the combined activities of two other proteins that prevented ZNF304 from being broken down in the cell. Mutant KRAS caused an increase in the levels of these two proteins, which in turn caused the elevated ZNF304 levels and the excessive marking of the DNA in the tumor suppressor genes. Furthermore, some of these same tumor suppressor genes are switched off in the earliest cells in a human embryo—which have the potential to become any of 200 or so cell types in the human body. In these embryonic stem cells, Serra, Fang et al. showed that ZNF304, but not KRAS, was also involved in keeping these genes switched off until the stem cells started changing into specific types of cells. Since they are a crucial part of the pathway linking a cancer-causing mutation to increased tumor growth, the proteins identified by Serra, Fang et al. could represent promising targets for the development of new anti-cancer drugs. DOI:http://dx.doi.org/10.7554/eLife.02313.002
Collapse
Affiliation(s)
- Ryan W Serra
- Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | | | | | | | | |
Collapse
|
29
|
Martin N, Raguz S, Dharmalingam G, Gil J. Co-regulation of senescence-associated genes by oncogenic homeobox proteins and polycomb repressive complexes. Cell Cycle 2014; 12:2194-9. [PMID: 24067365 DOI: 10.4161/cc.25331] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cellular senescence is a stable cell cycle arrest that can be induced by stresses such as telomere shortening, oncogene activation or DNA damage. Senescence is a potent anticancer barrier that needs to be circumvented during tumorigenesis. The cell cycle regulator p16(INK4a) is a key effector upregulated during senescence. Polycomb repressive complexes (PRCs) play a crucial role in silencing the INK4/ARF locus, which encodes for p16(INK4a), but the mechanisms by which PRCs are recruited to this locus as well as to other targets remain poorly understood. Recently we discovered the ability of the homeobox proteins HLX1 (H2.0-like homeobox 1) and HOXA9 (Homeobox A9) to bypass senescence. We showed that HLX1 and HOXA9 recruit PRCs to repress INK4a, which constitutes a key mechanism explaining their effects on senescence. Here we provide evidence for the regulation of additional senescence-associated PRC target genes by HLX1 and HOXA9. As both HLX1 and HOXA9 are oncogenes implicated in leukemogenesis, we discuss the implications that the collaboration between Homeobox proteins and PRCs has for senescence and cancer.
Collapse
Affiliation(s)
- Nadine Martin
- Cell Proliferation Group, MRC Clinical Sciences Centre, Imperial College London, London, UK
| | | | | | | |
Collapse
|
30
|
Patent Highlights. Pharm Pat Anal 2013. [DOI: 10.4155/ppa.13.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Snapshot of key developments in the patent literature accompanied by explanatory synopses
Collapse
|
31
|
Abstract
p16(INK4a), located on chromosome 9p21.3, is lost among a cluster of neighboring tumor suppressor genes. Although it is classically known for its capacity to inhibit cyclin-dependent kinase (CDK) activity, p16(INK4a) is not just a one-trick pony. Long-term p16(INK4a) expression pushes cells to enter senescence, an irreversible cell-cycle arrest that precludes the growth of would-be cancer cells but also contributes to cellular aging. Importantly, loss of p16(INK4a) is one of the most frequent events in human tumors and allows precancerous lesions to bypass senescence. Therefore, precise regulation of p16(INK4a) is essential to tissue homeostasis, maintaining a coordinated balance between tumor suppression and aging. This review outlines the molecular pathways critical for proper p16(INK4a) regulation and emphasizes the indispensable functions of p16(INK4a) in cancer, aging, and human physiology that make this gene special.
Collapse
Affiliation(s)
- Kyle M LaPak
- Biomedical Research Tower, Rm 586, The Ohio State University, 460 W. 12th Avenue, Columbus, OH 43210.
| | | |
Collapse
|
32
|
Zaina S, del Pilar Valencia-Morales M, Tristán-Flores FE, Lund G. Nuclear reprogramming and its role in vascular smooth muscle cells. Curr Atheroscler Rep 2013; 15:352. [PMID: 23881547 DOI: 10.1007/s11883-013-0352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In general terms, "nuclear reprogramming" refers to a change in gene expression profile that results in a significant switch in cellular phenotype. Nuclear reprogramming was first addressed by pioneering studies of cell differentiation during embryonic development. In recent years, nuclear reprogramming has been studied in great detail in the context of experimentally controlled dedifferentiation and transdifferentiation of mammalian cells for therapeutic purposes. In this review, we present a perspective on nuclear reprogramming in the context of spontaneous, pathophysiological phenotypic switch of vascular cells occurring in the atherosclerotic lesion. In particular, we focus on the current knowledge of epigenetic mechanisms participating in the extraordinary flexibility of the gene expression profile of vascular smooth muscle cells and other cell types participating in atherogenesis. Understanding how epigenetic changes participate in vascular cell plasticity may lead to effective therapies based on the remodelling of the vascular architecture.
Collapse
Affiliation(s)
- Silvio Zaina
- Department of Medical Sciences, Division of Health Sciences, León Campus, University of Guanajuato, 20 de Enero no. 929, 37320, León, Gto., Mexico.
| | | | | | | |
Collapse
|
33
|
Biochemical and functional interactions of human papillomavirus proteins with polycomb group proteins. Viruses 2013; 5:1231-49. [PMID: 23673719 PMCID: PMC3712305 DOI: 10.3390/v5051231] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 04/23/2013] [Accepted: 04/27/2013] [Indexed: 12/22/2022] Open
Abstract
The role of enzymes involved in polycomb repression of gene transcription has been studied extensively in human cancer. Polycomb repressive complexes mediate oncogene-induced senescence, a principal innate cell-intrinsic tumor suppressor pathway that thwarts expansion of cells that have suffered oncogenic hits. Infections with human cancer viruses including human papillomaviruses (HPVs) and Epstein-Barr virus can trigger oncogene-induced senescence, and the viruses have evolved strategies to abrogate this response in order to establish an infection and reprogram their host cells to establish a long-term persistent infection. As a consequence of inhibiting polycomb repression and evading oncogene induced-senescence, HPV infected cells have an altered epigenetic program as evidenced by aberrant homeobox gene expression. Similar alterations are frequently observed in non-virus associated human cancers and may be harnessed for diagnosis and therapy.
Collapse
|