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Kaller M, Forné I, Imhof A, Hermeking H. LINC01021 Attenuates Expression and Affects Alternative Splicing of a Subset of p53-Regulated Genes. Cancers (Basel) 2024; 16:1639. [PMID: 38730591 PMCID: PMC11083319 DOI: 10.3390/cancers16091639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Loss of the p53-inducible LINC01021 in p53-proficient CRC cell lines results in increased sensitivity to DNA-damaging chemotherapeutics. Here, we comprehensively analyze how LINC01021 affects the p53-induced transcriptional program. METHODS Using a CRISPR/Cas9-approach, we deleted the p53 binding site in the LINC01021 promoter of SW480 colorectal cancer cells and subjected them to RNA-Seq analysis after the activation of ectopic p53. RNA affinity purification followed by mass spectrometry was used to identify proteins associated with LINC01021. RESULTS Loss of the p53-inducibility of LINC01021 resulted in an ~1.8-fold increase in the number of significantly regulated mRNAs compared to LINC01021 wild-type cells after ectopic activation of p53. A subset of direct p53 target genes, such as NOXA and FAS, displayed significantly stronger induction when the p53-inducibility of LINC01021 was abrogated. Loss of the p53-inducibility of LINC01021 resulted in alternative splicing of a small number of mRNAs, such as ARHGAP12, HSF2, and LYN. Several RNA binding proteins involved in pre-mRNA splicing were identified as interaction partners of LINC01021 by mass spectrometry. CONCLUSIONS Our results suggest that LINC01021 may restrict the extent and strength of p53-mediated transcriptional changes via context-dependent regulation of the expression and splicing of a subset of p53-regulated genes.
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Affiliation(s)
- Markus Kaller
- Experimental and Molecular Pathology, Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Thalkirchner Strasse 36, D-80337 Munich, Germany
| | - Ignasi Forné
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, D-82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, D-82152 Planegg-Martinsried, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Thalkirchner Strasse 36, D-80337 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, D-69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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2
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Kow RL, Black AH, Henderson BP, Kraemer BC. Sut-6/NIPP1 modulates tau toxicity. Hum Mol Genet 2023; 32:2292-2306. [PMID: 37000013 PMCID: PMC10321383 DOI: 10.1093/hmg/ddad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/04/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
Neurodegenerative diseases exhibiting the pathological accumulation of tau such as Alzheimer's disease and related disorders still have no disease-modifying treatments and the molecular mechanisms of neurodegeneration remain unclear. To discover additional suppressor of tauopathy (sut) genes that mediate or modulate the toxicity of pathological tau, we performed a classical genetic screen using a tau transgenic Caenorhabditis elegans model. From this screen, we identified the suppressing mutation W292X in sut-6, the C. elegans homolog of human NIPP1, which truncates the C-terminal RNA-binding domain. Using CRISPR-based genome editing approaches, we generated null and additional C-terminally truncated alleles in sut-6 and found that loss of sut-6 or sut-6(W292X) suppresses tau-induced behavioral locomotor deficits, tau protein accumulation and neuron loss. The sut-6(W292X) mutation showed stronger and semi-dominant suppression of tau toxicity while sut-6 deletion acted recessively. Neuronal overexpression of SUT-6 protein did not significantly alter tau toxicity, but neuronal overexpression of SUT-6 W292X mutant protein reduced tau-mediated deficits. Epistasis studies showed tauopathy suppression by sut-6 occurs independent of other known nuclear speckle-localized suppressors of tau such as sut-2, aly-1/aly-3 and spop-1. In summary, we have shown that sut-6/NIPP1 modulates tau toxicity and found a dominant mutation in the RNA-binding domain of sut-6 which strongly suppresses tau toxicity. This suggests that altering RNA-related functions of SUT-6/NIPP1 instead of complete loss of SUT-6/NIPP1 will provide the strongest suppression of tau.
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Affiliation(s)
- R L Kow
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA 98104, USA
| | - A H Black
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
| | - B P Henderson
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
| | - B C Kraemer
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA 98104, USA
- Department of Psychiatry and Behavioral Sciences
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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3
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Deng J, Zhao HJ, Zhong Y, Hu C, Meng J, Wang C, Lan X, Wang X, Chen ZJ, Yan J, Wang W, Li Y. H3K27me3-modulated Hofbauer cell BMP2 signalling enhancement compensates for shallow trophoblast invasion in preeclampsia. EBioMedicine 2023; 93:104664. [PMID: 37331163 DOI: 10.1016/j.ebiom.2023.104664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND Preeclampsia (PE) is a common hypertensive pregnancy disorder associated with shallow trophoblast invasion. Although bone morphogenetic protein 2 (BMP2) has been shown to promote trophoblast invasion in vitro, its cellular origin and molecular regulation in placenta, as well as its potential role in PE, has yet to be established. Additionally, whether BMP2 and/or its downstream molecules could serve as potential diagnostic or therapeutic targets for PE has not been explored. METHODS Placentas and sera from PE and healthy pregnant women were subjected to multi-omics analyses, immunoblots, qPCR, and ELISA assays. Immortalized trophoblast cells, primary cultures of human trophoblasts, and first-trimester villous explants were used for in vitro experiments. Adenovirus expressing sFlt-1 (Ad Flt1)-induced PE rat model was used for in vivo studies. FINDINGS We find globally decreased H3K27me3 modifications and increased BMP2 signalling in preeclamptic placentas, which is negatively correlated with clinical manifestations. BMP2 is derived from Hofbauer cells and epigenetically regulated by H3K27me3 modification. BMP2 promotes trophoblast invasion and vascular mimicry by upregulating BMP6 via BMPR1A-SMAD2/3-SMAD4 signalling. BMP2 supplementation alleviates high blood pressure and fetal growth restriction phenotypes in Ad Flt1-induced rat PE model. INTERPRETATION Our findings demonstrate that epigenetically regulated Hofbauer cell-derived BMP2 signalling enhancement in late gestation could serve as a compensatory response for shallow trophoblast invasion in PE, suggesting opportunities for diagnostic marker and therapeutic target applications in PE clinical management. FUNDING National Key Research and Development Program of China (2022YFC2702400), National Natural Science Foundation of China (82101784, 82171648, 31988101), and Natural Science Foundation of Shandong Province (ZR2020QH051, ZR2020MH039).
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Affiliation(s)
- Jianye Deng
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China; Medical Integration and Practice Center, Shandong University, Jinan, Shandong, 250012, China
| | - Hong-Jin Zhao
- Department of Cardiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China; Department of Cardiology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Ying Zhong
- Cardiovascular Research Center of the General Medical Services, Massachusetts General Hospital, Boston, MA, 02129, USA
| | - Cuiping Hu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jinlai Meng
- Department of Obstetrics and Gynaecology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China
| | - Chunling Wang
- Department of Anesthesiology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiangxin Lan
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xiyao Wang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Junhao Yan
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China.
| | - Wei Wang
- Division of Neonatology, Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02115, USA.
| | - Yan Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China; Medical Integration and Practice Center, Shandong University, Jinan, Shandong, 250012, China.
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4
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Wright GM, Menzel J, Tatman PD, Black JC. Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539886. [PMID: 37214911 PMCID: PMC10197558 DOI: 10.1101/2023.05.08.539886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.
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5
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Schade AE, Kuzmickas R, Rodriguez CL, Mattioli K, Enos M, Gardner A, Cichowski K. Combating castration-resistant prostate cancer by co-targeting the epigenetic regulators EZH2 and HDAC. PLoS Biol 2023; 21:e3002038. [PMID: 37104245 PMCID: PMC10138213 DOI: 10.1371/journal.pbio.3002038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/16/2023] [Indexed: 04/28/2023] Open
Abstract
While screening and early detection have reduced mortality from prostate cancer, castration-resistant disease (CRPC) is still incurable. Here, we report that combined EZH2/HDAC inhibitors potently kill CRPCs and cause dramatic tumor regression in aggressive human and mouse CRPC models. Notably, EZH2 and HDAC both transmit transcriptional repressive signals: regulating histone H3 methylation and histone deacetylation, respectively. Accordingly, we show that suppression of both EZH2 and HDAC are required to derepress/induce a subset of EZH2 targets, by promoting the sequential demethylation and acetylation of histone H3. Moreover, we find that the induction of one of these targets, ATF3, which is a broad stress response gene, is critical for the therapeutic response. Importantly, in human tumors, low ATF3 levels are associated with decreased survival. Moreover, EZH2- and ATF3-mediated transcriptional programs inversely correlate and are most highly/lowly expressed in advanced disease. Together, these studies identify a promising therapeutic strategy for CRPC and suggest that these two major epigenetic regulators buffer prostate cancers from a lethal response to cellular stresses, thereby conferring a tractable therapeutic vulnerability.
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Affiliation(s)
- Amy E. Schade
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ryan Kuzmickas
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Carrie L. Rodriguez
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kaia Mattioli
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Miriam Enos
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alycia Gardner
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karen Cichowski
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts, United States of America
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6
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Farley SJ, Grishok A, Zeldich E. Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain. Epigenetics Chromatin 2022; 15:39. [PMID: 36463299 PMCID: PMC9719135 DOI: 10.1186/s13072-022-00471-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability is a well-known hallmark of Down Syndrome (DS) that results from the triplication of the critical region of human chromosome 21 (HSA21). Major studies were conducted in recent years to gain an understanding about the contribution of individual triplicated genes to DS-related brain pathology. Global transcriptomic alterations and widespread changes in the establishment of neural lineages, as well as their differentiation and functional maturity, suggest genome-wide chromatin organization alterations in trisomy. High Mobility Group Nucleosome Binding Domain 1 (HMGN1), expressed from HSA21, is a chromatin remodeling protein that facilitates chromatin decompaction and is associated with acetylated lysine 27 on histone H3 (H3K27ac), a mark correlated with active transcription. Recent studies causatively linked overexpression of HMGN1 in trisomy and the development of DS-associated B cell acute lymphoblastic leukemia (B-ALL). HMGN1 has been shown to antagonize the activity of the Polycomb Repressive Complex 2 (PRC2) and prevent the deposition of histone H3 lysine 27 trimethylation mark (H3K27me3), which is associated with transcriptional repression and gene silencing. However, the possible ramifications of the increased levels of HMGN1 through the derepression of PRC2 target genes on brain cell pathology have not gained attention. In this review, we discuss the functional significance of HMGN1 in brain development and summarize accumulating reports about the essential role of PRC2 in the development of the neural system. Mechanistic understanding of how overexpression of HMGN1 may contribute to aberrant brain cell phenotypes in DS, such as altered proliferation of neural progenitors, abnormal cortical architecture, diminished myelination, neurodegeneration, and Alzheimer's disease-related pathology in trisomy 21, will facilitate the development of DS therapeutic approaches targeting chromatin.
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Affiliation(s)
- Sean J. Farley
- grid.189504.10000 0004 1936 7558Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Alla Grishok
- grid.189504.10000 0004 1936 7558Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA ,grid.189504.10000 0004 1936 7558Boston University Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Ella Zeldich
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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7
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Dolatabadi S, Jonasson E, Andersson L, Luna Santamaría M, Lindén M, Österlund T, Åman P, Ståhlberg A. FUS-DDIT3 Fusion Oncoprotein Expression Affects JAK-STAT Signaling in Myxoid Liposarcoma. Front Oncol 2022; 12:816894. [PMID: 35186752 PMCID: PMC8851354 DOI: 10.3389/fonc.2022.816894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/06/2022] [Indexed: 11/25/2022] Open
Abstract
Myxoid liposarcoma is one of the most common sarcoma entities characterized by FET fusion oncogenes. Despite a generally favorable prognosis of myxoid liposarcoma, chemotherapy resistance remains a clinical problem. This cancer stem cell property is associated with JAK-STAT signaling, but the link to the myxoid-liposarcoma-specific FET fusion oncogene FUS-DDIT3 is not known. Here, we show that ectopic expression of FUS-DDIT3 resulted in elevated levels of STAT3 and phosphorylated STAT3. RNA sequencing identified 126 genes that were regulated by both FUS-DDIT3 expression and JAK1/2 inhibition using ruxolitinib. Sixty-six of these genes were connected in a protein interaction network. Fifty-three and 29 of these genes were confirmed as FUS-DDIT3 and STAT3 targets, respectively, using public chromatin immunoprecipitation sequencing data sets. Enriched gene sets among the 126 regulated genes included processes related to cytokine signaling, adipocytokine signaling, and chromatin remodeling. We validated CD44 as a target gene of JAK1/2 inhibition and as a potential cancer stem cell marker in myxoid liposarcoma. Finally, we showed that FUS-DDIT3 interacted with phosphorylated STAT3 in association with subunits of the SWI/SNF chromatin remodeling complex and PRC2 repressive complex. Our data show that the function of FUS-DDIT3 is closely connected to JAK-STAT signaling. Detailed deciphering of molecular mechanisms behind tumor progression opens up new avenues for targeted therapies in sarcomas and leukemia characterized by FET fusion oncogenes.
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Affiliation(s)
- Soheila Dolatabadi
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Emma Jonasson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Lisa Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Manuel Luna Santamaría
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Malin Lindén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Pierre Åman
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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8
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Di Pietro A, Polmear J, Cooper L, Damelang T, Hussain T, Hailes L, O'Donnell K, Udupa V, Mi T, Preston S, Shtewe A, Hershberg U, Turner SJ, La Gruta NL, Chung AW, Tarlinton DM, Scharer CD, Good-Jacobson KL. Targeting BMI-1 in B cells restores effective humoral immune responses and controls chronic viral infection. Nat Immunol 2022; 23:86-98. [PMID: 34845392 DOI: 10.1038/s41590-021-01077-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 10/20/2021] [Indexed: 01/12/2023]
Abstract
Ineffective antibody-mediated responses are a key characteristic of chronic viral infection. However, our understanding of the intrinsic mechanisms that drive this dysregulation are unclear. Here, we identify that targeting the epigenetic modifier BMI-1 in mice improves humoral responses to chronic lymphocytic choriomeningitis virus. BMI-1 was upregulated by germinal center B cells in chronic viral infection, correlating with changes to the accessible chromatin landscape, compared to acute infection. B cell-intrinsic deletion of Bmi1 accelerated viral clearance, reduced splenomegaly and restored splenic architecture. Deletion of Bmi1 restored c-Myc expression in B cells, concomitant with improved quality of antibody and coupled with reduced antibody-secreting cell numbers. Specifically, BMI-1-deficiency induced antibody with increased neutralizing capacity and enhanced antibody-dependent effector function. Using a small molecule inhibitor to murine BMI-1, we could deplete antibody-secreting cells and prohibit detrimental immune complex formation in vivo. This study defines BMI-1 as a crucial immune modifier that controls antibody-mediated responses in chronic infection.
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Affiliation(s)
- Andrea Di Pietro
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jack Polmear
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Lucy Cooper
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Timon Damelang
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Tabinda Hussain
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Lauren Hailes
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kristy O'Donnell
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, Victoria, Australia
| | - Vibha Udupa
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.,Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Tian Mi
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Simon Preston
- Divisions of Immunology and Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Areen Shtewe
- Department of Human Biology, Faculty of Science, University of Haifa, Haifa, Israel
| | - Uri Hershberg
- Department of Human Biology, Faculty of Science, University of Haifa, Haifa, Israel
| | - Stephen J Turner
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Amy W Chung
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - David M Tarlinton
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, Victoria, Australia
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia. .,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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9
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Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes. Nat Commun 2021; 12:6276. [PMID: 34725325 PMCID: PMC8560912 DOI: 10.1038/s41467-021-26502-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a collection of biologically diverse cancers characterized by distinct transcriptional patterns, biology, and immune composition. TNBCs subtypes include two basal-like (BL1, BL2), a mesenchymal (M) and a luminal androgen receptor (LAR) subtype. Through a comprehensive analysis of mutation, copy number, transcriptomic, epigenetic, proteomic, and phospho-proteomic patterns we describe the genomic landscape of TNBC subtypes. Mesenchymal subtype tumors display high mutation loads, genomic instability, absence of immune cells, low PD-L1 expression, decreased global DNA methylation, and transcriptional repression of antigen presentation genes. We demonstrate that major histocompatibility complex I (MHC-I) is transcriptionally suppressed by H3K27me3 modifications by the polycomb repressor complex 2 (PRC2). Pharmacological inhibition of PRC2 subunits EZH2 or EED restores MHC-I expression and enhances chemotherapy efficacy in murine tumor models, providing a rationale for using PRC2 inhibitors in PD-L1 negative mesenchymal tumors. Subtype-specific differences in immune cell composition and differential genetic/pharmacological vulnerabilities suggest additional treatment strategies for TNBC. Triple negative breast cancer can be divided into additional subtypes. Here, using omics analyses, the authors show that in the mesenchymal subtype expression of MHC-1 is repressed and that this can be restored by using drugs that target subunits of the epigenetic modifier PRC2.
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10
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Fraser M, Livingstone J, Wrana JL, Finelli A, He HH, van der Kwast T, Zlotta AR, Bristow RG, Boutros PC. Somatic driver mutation prevalence in 1844 prostate cancers identifies ZNRF3 loss as a predictor of metastatic relapse. Nat Commun 2021; 12:6248. [PMID: 34716314 PMCID: PMC8556363 DOI: 10.1038/s41467-021-26489-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Driver gene mutations that are more prevalent in metastatic, castration-resistant prostate cancer (mCRPC) than localized disease represent candidate prognostic biomarkers. We analyze 1,844 localized (1,289) or mCRPC (555) tumors and quantify the prevalence of 113 somatic driver single nucleotide variants (SNVs), copy number aberrations (CNAs), and structural variants (SVs) in each state. One-third are significantly more prevalent in mCRPC than expected while a quarter are less prevalent. Mutations in AR and its enhancer are more prevalent in mCRPC, as are those in TP53, MYC, ZNRF3 and PRKDC. ZNRF3 loss is associated with decreased ZNRF3 mRNA abundance, WNT, cell cycle & PRC1/2 activity, and genomic instability. ZNRF3 loss, RNA downregulation and hypermethylation are prognostic of metastasis and overall survival, independent of clinical and pathologic indices. These data demonstrate a strategy for identifying biomarkers of localized cancer aggression, with ZNRF3 loss as a predictor of metastasis in prostate cancer.
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Affiliation(s)
- Michael Fraser
- grid.17063.330000 0001 2157 2938Department of Surgery, Division of Urology, University of Toronto, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XDepartment of Surgical Oncology, Genitourinary Site Group, Princess Margaret Cancer Centre, Toronto, ON Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, ON Canada
| | - Julie Livingstone
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Urology, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Institute for Precision Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA USA
| | - Jeffrey L. Wrana
- grid.416166.20000 0004 0473 9881Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON Canada ,grid.492573.eMount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Antonio Finelli
- grid.17063.330000 0001 2157 2938Department of Surgery, Division of Urology, University of Toronto, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XDepartment of Surgical Oncology, Genitourinary Site Group, Princess Margaret Cancer Centre, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XPrincess Margaret Cancer Centre, Toronto, ON Canada
| | - Housheng Hansen He
- grid.415224.40000 0001 2150 066XPrincess Margaret Cancer Centre, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, ON Canada
| | - Theodorus van der Kwast
- grid.17063.330000 0001 2157 2938Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428Laboratory Medicine Program, University Health Network, Toronto, ON Canada
| | - Alexandre R. Zlotta
- grid.17063.330000 0001 2157 2938Department of Surgery, Division of Urology, University of Toronto, Toronto, ON Canada ,grid.415224.40000 0001 2150 066XDepartment of Surgical Oncology, Genitourinary Site Group, Princess Margaret Cancer Centre, Toronto, ON Canada ,grid.416166.20000 0004 0473 9881Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON Canada ,grid.492573.eMount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Robert G. Bristow
- grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, ON Canada ,Manchester Cancer Research Centre, Manchester, UK ,grid.5379.80000000121662407University of Manchester, Manchester, UK
| | - Paul C. Boutros
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Urology, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Institute for Precision Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA USA ,grid.17063.330000 0001 2157 2938Department of Medical Biophysics, University of Toronto, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON Canada
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Hanaki S, Habara M, Masaki T, Maeda K, Sato Y, Nakanishi M, Shimada M. PP1 regulatory subunit NIPP1 regulates transcription of E2F1 target genes following DNA damage. Cancer Sci 2021; 112:2739-2752. [PMID: 33939241 PMCID: PMC8253265 DOI: 10.1111/cas.14924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
DNA damage induces transcriptional repression of E2F1 target genes and a reduction in histone H3‐Thr11 phosphorylation (H3‐pThr11) at E2F1 target gene promoters. Dephosphorylation of H3‐pThr11 is partly mediated by Chk1 kinase and protein phosphatase 1γ (PP1γ) phosphatase. Here, we isolated NIPP1 as a regulator of PP1γ‐mediated H3‐pThr11 by surveying nearly 200 PP1 interactor proteins. We found that NIPP1 inhibits PP1γ‐mediated dephosphorylation of H3‐pThr11 both in vivo and in vitro. By generating NIPP1‐depleted cells, we showed that NIPP1 is required for cell proliferation and the expression of E2F1 target genes. Upon DNA damage, activated protein kinase A (PKA) phosphorylated the NIPP1‐Ser199 residue, adjacent to the PP1 binding motif (RVxF), and triggered the dissociation of NIPP1 from PP1γ, leading to the activation of PP1γ. Furthermore, the inhibition of PKA activity led to the activation of E2F target genes. Statistical analysis confirmed that the expression of NIPP1 was positively correlated with E2F target genes. Taken together, these findings demonstrate that the PP1 regulatory subunit NIPP1 modulates E2F1 target genes by linking PKA and PP1γ during DNA damage.
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Affiliation(s)
- Shunsuke Hanaki
- Department of Biochemistry, Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Makoto Habara
- Department of Biochemistry, Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Takahiro Masaki
- Department of Biochemistry, Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Keisuke Maeda
- Department of Biochemistry, Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Yuki Sato
- Department of Biochemistry, Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Makoto Nakanishi
- Division of Cancer Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Midori Shimada
- Department of Biochemistry, Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
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12
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Alsharif I, Boukhzar L, Lefranc B, Godefroy D, Aury-Landas J, Rego JLD, Rego JCD, Naudet F, Arabo A, Chagraoui A, Maltête D, Benazzouz A, Baugé C, Leprince J, Elkahloun AG, Eiden LE, Anouar Y. Cell-penetrating, antioxidant SELENOT mimetic protects dopaminergic neurons and ameliorates motor dysfunction in Parkinson's disease animal models. Redox Biol 2021; 40:101839. [PMID: 33486153 PMCID: PMC7823055 DOI: 10.1016/j.redox.2020.101839] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by motor dysfunction for which there is an unmet need for better treatment options. Although oxidative stress is a common feature of neurodegenerative diseases, notably PD, there is currently no efficient therapeutic strategy able to tackle this multi-target pathophysiological process. Based on our previous observations of the potent antioxidant and neuroprotective activity of SELENOT, a vital thioredoxin-like selenoprotein, we designed the small peptide PSELT from its redox active site to evaluate its antioxidant properties in vivo, and its potential polyfunctional activity in PD models. PSELT protects neurotoxin-treated dopaminergic neurons against oxidative stress and cell death, and their fibers against neurotoxic degeneration. PSELT is cell-permeable and acts in multiple subcellular compartments of dopaminergic neurons that are vulnerable to oxidative stress. In rodent models of PD, this protective activity prevented neurodegeneration, restored phosphorylated tyrosine hydroxylase levels, and led to improved motor skills. Transcriptomic analysis revealed that gene regulation by PSELT after MPP+ treatment negatively correlates with that occurring in PD, and positively correlates with that occurring after resveratrol treatment. Mechanistically, a major impact of PSELT is via nuclear stimulation of the transcription factor EZH2, leading to neuroprotection. Overall, these findings demonstrate the potential of PSELT as a therapeutic candidate for treatment of PD, targeting oxidative stress at multiple intracellular levels.
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Affiliation(s)
- Ifat Alsharif
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France; Biology department, Jamoum University College, Umm Alqura University, Saudi Arabia
| | - Loubna Boukhzar
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France
| | - Benjamin Lefranc
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France; PRIMACEN, Cell Imaging Platform of Normandie, UNIROUEN, 76000, Rouen, France
| | - David Godefroy
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France
| | | | - Jean-Luc do Rego
- Institute for Research and Innovation in Biomedicine, 76000, Rouen, France; Behavioral Analysis Platform SCAC, Rouen Medical School, Rouen Normandie University, 76183, Rouen, France
| | - Jean-Claude do Rego
- Institute for Research and Innovation in Biomedicine, 76000, Rouen, France; Behavioral Analysis Platform SCAC, Rouen Medical School, Rouen Normandie University, 76183, Rouen, France
| | - Frédéric Naudet
- Institut des Maladies Neurodégénératives, CNRS, UMR 5293, Bordeaux University, F-33000, Bordeaux, France
| | - Arnaud Arabo
- Biological Resource Service (SRB), Faculty of Sciences and Techniques, Rouen Normandie University, 76821, Mont-Saint-Aignan, France
| | - Abdeslam Chagraoui
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France
| | - David Maltête
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France
| | - Abdelhamid Benazzouz
- Institut des Maladies Neurodégénératives, CNRS, UMR 5293, Bordeaux University, F-33000, Bordeaux, France
| | | | - Jérôme Leprince
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France; PRIMACEN, Cell Imaging Platform of Normandie, UNIROUEN, 76000, Rouen, France
| | - Abdel G Elkahloun
- Comparative Genomics and Cancer, Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lee E Eiden
- Section on Molecular Neuroscience, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Youssef Anouar
- UNIROUEN, Inserm U1239, Neuronal and Neuroendocrine Differentiation and Communication Laboratory, Rouen Normandie University, 76821, Mont-Saint-Aignan, France; Institute for Research and Innovation in Biomedicine, 76000, Rouen, France.
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Implication of EZH2 in the Pro-Proliferative and Apoptosis-Resistant Phenotype of Pulmonary Artery Smooth Muscle Cells in PAH: A Transcriptomic and Proteomic Approach. Int J Mol Sci 2021; 22:ijms22062957. [PMID: 33803922 PMCID: PMC7999120 DOI: 10.3390/ijms22062957] [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: 02/18/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 12/13/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a progressive disorder characterized by a sustained elevation of pulmonary artery (PA) pressure, right ventricular failure, and premature death. Enhanced proliferation and resistance to apoptosis (as seen in cancer cells) of PA smooth muscle cells (PASMCs) is a major pathological hallmark contributing to pulmonary vascular remodeling in PAH, for which current therapies have only limited effects. Emerging evidence points toward a critical role for Enhancer of Zeste Homolog 2 (EZH2) in cancer cell proliferation and survival. However, its role in PAH remains largely unknown. The aim of this study was to determine whether EZH2 represents a new factor critically involved in the abnormal phenotype of PAH-PASMCs. We found that EZH2 is overexpressed in human lung tissues and isolated PASMCs from PAH patients compared to controls as well as in two animal models mimicking the disease. Through loss- and gain-of-function approaches, we showed that EZH2 promotes PAH-PASMC proliferation and survival. By combining quantitative transcriptomic and proteomic approaches in PAH-PASMCs subjected or not to EZH2 knockdown, we found that inhibition of EZH2 downregulates many factors involved in cell-cycle progression, including E2F targets, and contributes to maintain energy production. Notably, we found that EZH2 promotes expression of several nuclear-encoded components of the mitochondrial translation machinery and tricarboxylic acid cycle genes. Overall, this study provides evidence that, by overexpressing EZH2, PAH-PASMCs remove the physiological breaks that normally restrain their proliferation and susceptibility to apoptosis and suggests that EZH2 or downstream factors may serve as therapeutic targets to combat pulmonary vascular remodeling.
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Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer. Nat Commun 2021; 12:1628. [PMID: 33712615 PMCID: PMC7955121 DOI: 10.1038/s41467-021-21884-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/22/2021] [Indexed: 01/31/2023] Open
Abstract
Tyrosine kinase inhibitors were found to be clinically effective for treatment of patients with certain subsets of cancers carrying somatic mutations in receptor tyrosine kinases. However, the duration of clinical response is often limited, and patients ultimately develop drug resistance. Here, we use single-cell RNA sequencing to demonstrate the existence of multiple cancer cell subpopulations within cell lines, xenograft tumors and patient tumors. These subpopulations exhibit epigenetic changes and differential therapeutic sensitivity. Recurrently overrepresented ontologies in genes that are differentially expressed between drug tolerant cell populations and drug sensitive cells include epithelial-to-mesenchymal transition, epithelium development, vesicle mediated transport, drug metabolism and cholesterol homeostasis. We show analysis of identified markers using the LINCS database to predict and functionally validate small molecules that target selected drug tolerant cell populations. In combination with EGFR inhibitors, crizotinib inhibits the emergence of a defined subset of EGFR inhibitor-tolerant clones. In this study, we describe the spectrum of changes associated with drug tolerance and inhibition of specific tolerant cell subpopulations with combination agents.
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15
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Gravelle P, Jean C, Valleron W, Laurent G, Fournié JJ. Innate predisposition to immune escape in follicular lymphoma cells. Oncoimmunology 2021; 1:555-556. [PMID: 22754785 PMCID: PMC3382883 DOI: 10.4161/onci.19365] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Tumor-intrinsic immuno-resistance is a prerequisite for emergence of follicular lymphomas. Here we show that in vitro, such cells are more resistant to immune cytolysis when grown as follicle-mimicking tridimensional aggregates than when grown as cell suspensions. So in patients, this innate adaptation to tumor immunity might precede its selective pressure.
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Affiliation(s)
- Pauline Gravelle
- INSERM UMR1037; Cancer Research Center of Toulouse; Toulouse, France ; Université Toulouse III Paul-Sabatier; Toulouse, France ; ERL 5294 CNRS, BP3028, Hospital Purpan; Toulouse, France
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LncRNA Profiling Reveals That the Deregulation of H19, WT1-AS, TCL6, and LEF1-AS1 Is Associated with Higher-Risk Myelodysplastic Syndrome. Cancers (Basel) 2020; 12:cancers12102726. [PMID: 32977510 PMCID: PMC7598221 DOI: 10.3390/cancers12102726] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Although lncRNAs have been increasingly recognized as regulators of hematopoiesis, only several studies addressed their role in myelodysplastic syndrome (MDS). By genome-wide profiling, we identified lncRNAs deregulated in various groups of MDS patients. We computationally constructed lncRNA-protein coding gene networks to associate deregulated lncRNAs with cellular processes involved in MDS. We showed that expression of H19, WT1-AS, TCL6, and LEF1-AS1 lncRNAs associate with higher-risk MDS and proposed processes related with these transcripts. Abstract Background: myelodysplastic syndrome (MDS) is a hematopoietic stem cell disorder with an incompletely known pathogenesis. Long noncoding RNAs (lncRNAs) play multiple roles in hematopoiesis and represent a new class of biomarkers and therapeutic targets, but information on their roles in MDS is limited. Aims: here, we aimed to characterize lncRNAs deregulated in MDS that may function in disease pathogenesis. In particular, we focused on the identification of lncRNAs that could serve as novel potential biomarkers of adverse outcomes in MDS. Methods: we performed microarray expression profiling of lncRNAs and protein-coding genes (PCGs) in the CD34+ bone marrow cells of MDS patients. Expression profiles were analyzed in relation to different aspects of the disease (i.e., diagnosis, disease subtypes, cytogenetic and mutational aberrations, and risk of progression). LncRNA-PCG networks were constructed to link deregulated lncRNAs with regulatory mechanisms associated with MDS. Results: we found several lncRNAs strongly associated with disease pathogenesis (e.g., H19, WT1-AS, TCL6, LEF1-AS1, EPB41L4A-AS1, PVT1, GAS5, and ZFAS1). Of these, downregulation of LEF1-AS1 and TCL6 and upregulation of H19 and WT1-AS were associated with adverse outcomes in MDS patients. Multivariate analysis revealed that the predominant variables predictive of survival are blast count, H19 level, and TP53 mutation. Coexpression network data suggested that prognosis-related lncRNAs are predominantly related to cell adhesion and differentiation processes (H19 and WT1-AS) and mechanisms such as chromatin modification, cytokine response, and cell proliferation and death (LEF1-AS1 and TCL6). In addition, we observed that transcriptional regulation in the H19/IGF2 region is disrupted in higher-risk MDS, and discordant expression in this locus is associated with worse outcomes. Conclusions: we identified specific lncRNAs contributing to MDS pathogenesis and proposed cellular processes associated with these transcripts. Of the lncRNAs associated with patient prognosis, the level of H19 transcript might serve as a robust marker comparable to the clinical variables currently used for patient stratification.
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Liebisch M, Wolf G. AGE-Induced Suppression of EZH2 Mediates Injury of Podocytes by Reducing H3K27me3. Am J Nephrol 2020; 51:676-692. [PMID: 32854097 DOI: 10.1159/000510140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/12/2020] [Indexed: 01/11/2023]
Abstract
BACKGROUND Chronic hyperglycemia, a pivotal feature of diabetes mellitus (DM), initiates the formation of advanced glycation end products (AGEs) and the dysregulation of epigenetic mechanisms, which may cause injury to renal podocytes, a central feature of diabetic kidney disease (DKD). Previous data of our group showed that AGEs significantly reduce the expression of NIPP1 (nuclear inhibitor of protein phosphatase 1) in podocytes in vitro as well as in human and murine DKD. NIPP1 was shown by others to interact with enhancer of zeste homolog 2 (EZH2), which catalyzes the repressive methylation of H3K27me3 on histone 3. Therefore, we hypothesized that AGEs can directly induce epigenetic changes in podocytes. METHODS We analyzed the relevance of AGEs on EZH2 expression and activity in a murine podocyte cell line. Cells were treated with 5 mg/mL glycated BSA for 24 h. To determine the meaning of EZH2 suppression, EZH2 activity was inhibited by incubating the cells with the pharmacological methyltransferase inhibitor 3-deazaneplanocin A; EZH2 expression was repressed with siRNA. mRNA expression was analyzed with real-time PCR, and protein expression with Western blot. EZH2 expression and level of H3K27 trimethylation in podocytes of diabetic db/db mice, a mouse model for type 2 DM, were analyzed using immunofluorescence. RESULTS Our data demonstrated that AGEs decrease EZH2 expression in podocytes and consequently reduce H3K27me3. This suppression of EZH2 mimicked the AGE effects and caused an upregulated expression of pathological factors that contribute to podocyte injury in DKD. In addition, analyses of db/db mice showed significantly reduced H3K27me3 and EZH2 expression in podocytes. Moreover, the suppression of NIPP1 and EZH2 showed similar effects regarding podocyte injury. CONCLUSIONS Our studies provide a novel pathway how AGEs contribute to podocyte injury and the formation of the so-called metabolic memory in DKD.
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Affiliation(s)
- Marita Liebisch
- Department of Internal Medicine III, University Hospital Jena, Jena, Germany
| | - Gunter Wolf
- Department of Internal Medicine III, University Hospital Jena, Jena, Germany,
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18
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Zhao Y, Yu T, Chen L, Xie D, Wang F, Fu L, Cheng C, Li Y, Zhu X, Miao G. A Germline CHEK2 Mutation in a Family with Papillary Thyroid Cancer. Thyroid 2020; 30:924-930. [PMID: 32041497 DOI: 10.1089/thy.2019.0774] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Approximately 5% of all cases of papillary thyroid cancer (PTC) are inherited. However, the susceptibility gene(s) for nonsyndromic familial PTC (FPTC) remain unclear. We performed whole genome sequencing of peripheral blood DNA samples from two affected family members with PTC. CHEK2 transcript expression and the protein levels of CHK2 and p53 were evaluated in the thyroid tissues from two affected members of the kindred and sporadic PTC cases. The entire CHEK2 coding sequence was examined by Sanger sequencing in blood DNA samples from 242 sporadic PTC patients. We identified a novel heterozygous germline mutation in CHEK2 (c.417C→A) that was detected in all available affected members of a kindred with FPTC. This variant was found in only 1 out of 264,200 persons in the Genome Aggregation Database and the NHLBI Trans-Omics for Precision Medicine program. The CHEK2 c.417C→A variant introduces a premature termination codon (Y139X). We found reduced CHK2 protein expression in tumor samples from the two patients who carried the variant as compared with sporadic cases without the variant. The Y139X loss-of-function variant led to reduced p53 phosphorylation and decreased p53 protein level. In addition, two rare missense variants (R180C and H371Y) in CHEK2 were identified in 5 (2%) of 242 patients with sporadic PTC. Our findings suggest that the CHEK2 Y139X variant may be associated with FPTC.
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Affiliation(s)
- Yanyang Zhao
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
- The Chinese Academy of Medical Sciences, Beijing, China
| | - Tian Yu
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Lan Chen
- Department of Pathology, Beijing Hospital, Ministry of Health, Beijing, China
| | - Donghui Xie
- Department of General Surgery, Beijing Hospital, Ministry of Health, Beijing, China
| | - Feiliang Wang
- Department of Ultrasonography, Beijing Hospital, Ministry of Health, Beijing, China
| | - Liping Fu
- Department of General Surgery, Beijing Hospital, Ministry of Health, Beijing, China
| | - Chaoze Cheng
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Yao Li
- Department of General Surgery, Beijing Hospital, Ministry of Health, Beijing, China
| | - Xiaoquan Zhu
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Gang Miao
- Department of General Surgery, Beijing Hospital, Ministry of Health, Beijing, China
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Enhanced DNA-repair capacity and resistance to chemically induced carcinogenesis upon deletion of the phosphatase regulator NIPP1. Oncogenesis 2020; 9:30. [PMID: 32123159 PMCID: PMC7051951 DOI: 10.1038/s41389-020-0214-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022] Open
Abstract
Nuclear Inhibitor of PP1 (NIPP1) is a conserved regulatory subunit of protein phosphatase PP1. The selective deletion of NIPP1 in mouse liver parenchymal cells or skin epidermal cells culminates in a late-onset hyperproliferation of a subset of resident progenitor cells. Although a hyperplastic phenotype is usually tumor promoting, we show here that the absence of NIPP1 conferred a strong resistance to chemically induced hepatocellular or skin carcinoma. The ablation of NIPP1 did not affect the metabolism of the administered mutagens (diethylnitrosamine or 7,12-dimethylbenz[a]anthracene), but reduced the conversion of mutagen-induced covalent DNA modifications into cancer-initiating mutations. This reduced sensitivity to mutagens correlated with an enhanced DNA-damage response and an augmented expression of rate-limiting DNA-repair proteins (MGMT in liver, XPD and XPG in skin), hinting at an increased DNA-repair capacity. Our data identify NIPP1 as a repressor of DNA repair and as a promising target for novel cancer prevention and treatment therapies.
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20
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Phosphatase Regulator NIPP1 Restrains Chemokine-Driven Skin Inflammation. J Invest Dermatol 2020; 140:1576-1588. [PMID: 31972250 DOI: 10.1016/j.jid.2020.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/20/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023]
Abstract
Nuclear inhibitor of protein phosphatase 1 (NIPP1) is a ubiquitously expressed nuclear protein that regulates functions of protein serine/threonine phosphatase-1 in cell proliferation and lineage specification. The role of NIPP1 in tissue homeostasis is not fully understood. This study shows that the selective deletion of NIPP1 in mouse epidermis resulted in epidermal hyperproliferation, a reduced adherence of basal keratinocytes, and a gradual decrease in the stemness of hair follicle stem cells, culminating in hair loss. This complex phenotype was associated with chronic sterile skin inflammation and could be partially rescued by dexamethasone treatment. NIPP1-deficient keratinocytes massively expressed proinflammatory chemokines and immunomodulatory proteins in a cell-autonomous manner. Chemokines subsequently induced the recruitment and activation of immune cells, in particular conventional dendritic cells and Langerhans cells, accounting for the chronic inflammation phenotype. The data identifies NIPP1 as a key regulator of epidermal homeostasis and as a potential target for the treatment of inflammatory skin diseases.
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Tang J, Yu B, Li Y, Zhang W, Alvarez AA, Hu B, Cheng S, Feng H. TGF-β-activated lncRNA LINC00115 is a critical regulator of glioma stem-like cell tumorigenicity. EMBO Rep 2019; 20:e48170. [PMID: 31599491 PMCID: PMC6893290 DOI: 10.15252/embr.201948170] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are critical regulators in cancer. However, the involvement of lncRNAs in TGF-β-regulated tumorigenicity is still unclear. Here, we identify TGF-β-activated lncRNA LINC00115 as a critical regulator of glioma stem-like cell (GSC) self-renewal and tumorigenicity. LINC00115 is upregulated by TGF-β, acts as a miRNA sponge, and upregulates ZEB1 by competitively binding of miR-200s, thereby enhancing ZEB1 signaling and GSC self-renewal. LINC00115 also promotes ZNF596 transcription by preventing binding of miR-200s to the 5'-UTR of ZNF596, resulting in augmented ZNF596/EZH2/STAT3 signaling and GBM tumor growth. Inhibition of EZH2 by genetic approaches or a small molecular inhibitor markedly suppresses LINC00115-driven GSC self-renewal and tumorigenicity. Moreover, LINC00115 is highly expressed in GBM, and LINC00115 expression or correlated co-expression with ZEB1 or ZNF596 is prognostic for clinical GBM survival. Our work defines a critical role of LINC00115 in GSC self-renewal and tumorigenicity, and suggests LINC00115 as a potential target for GBM treatment.
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Affiliation(s)
- Jianming Tang
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Bo Yu
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Yanxin Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of HealthDepartment of Hematology & OncologyShanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Weiwei Zhang
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
| | - Angel A Alvarez
- Department of NeurologyNorthwestern Brain Tumor InstituteThe Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Bo Hu
- Department of NeurologyNorthwestern Brain Tumor InstituteThe Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Shi‐Yuan Cheng
- Department of NeurologyNorthwestern Brain Tumor InstituteThe Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Haizhong Feng
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterShanghai Cancer InstituteRen Ji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina
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22
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Reale E, Taverna D, Cantini L, Martignetti L, Osella M, De Pittà C, Virga F, Orso F, Caselle M. Investigating the epi-miRNome: identification of epi-miRNAs using transfection experiments. Epigenomics 2019; 11:1581-1599. [PMID: 31693439 DOI: 10.2217/epi-2019-0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Growing evidence shows a strong interplay between post-transcriptional regulation, mediated by miRNAs (miRs) and epigenetic regulation. Nevertheless, the number of experimentally validated miRs (called epi-miRs) involved in these regulatory circuitries is still very small. Material & methods: We propose a pipeline to prioritize candidate epi-miRs and to identify potential epigenetic interactors of any given miR starting from miR transfection experiment datasets. Results & conclusion: We identified 34 candidate epi-miRs: 19 of them are known epi-miRs, while 15 are new. Moreover, using an in-house generated gene expression dataset, we experimentally proved that a component of the polycomb-repressive complex 2, the histone methyltransferase enhancer of zeste homolog 2 (EZH2), interacts with miR-214, a well-known prometastatic miR in melanoma and breast cancer, highlighting a miR-214-EZH2 regulatory axis potentially relevant in tumor progression.
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Affiliation(s)
- Elisa Reale
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
| | - Daniela Taverna
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy.,Center for Complex Systems in Molecular Biology & Medicine, University of Torino, 10123, Torino, Italy
| | - Laura Cantini
- Institut Curie, PSL Research University, INSERM U900, Paris, France.,Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, 75005 Paris, France
| | | | - Matteo Osella
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
| | | | - Federico Virga
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy
| | - Francesca Orso
- Molecular Biotechnology Center (MBC), 10126, Torino, Italy.,Department of Molecular Biotechnology & Health Sciences, 10126, Torino, Italy.,Center for Complex Systems in Molecular Biology & Medicine, University of Torino, 10123, Torino, Italy
| | - Michele Caselle
- Department of Physics & INFN, University of Torino, 10125, Torino, Italy
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23
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Donaldson-Collier MC, Sungalee S, Zufferey M, Tavernari D, Katanayeva N, Battistello E, Mina M, Douglass KM, Rey T, Raynaud F, Manley S, Ciriello G, Oricchio E. EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains. Nat Genet 2019; 51:517-528. [PMID: 30692681 DOI: 10.1038/s41588-018-0338-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/17/2018] [Indexed: 12/16/2022]
Abstract
Chromatin is organized into topologically associating domains (TADs) enriched in distinct histone marks. In cancer, gain-of-function mutations in the gene encoding the enhancer of zeste homolog 2 protein (EZH2) lead to a genome-wide increase in histone-3 Lys27 trimethylation (H3K27me3) associated with transcriptional repression. However, the effects of these epigenetic changes on the structure and function of chromatin domains have not been explored. Here, we found a functional interplay between TADs and epigenetic and transcriptional changes mediated by mutated EZH2. Altered EZH2 (p.Tyr646* (EZH2Y646X)) led to silencing of entire domains, synergistically inactivating multiple tumor suppressors. Intra-TAD gene silencing was coupled with changes of interactions between gene promoter regions. Notably, gene expression and chromatin interactions were restored by pharmacological inhibition of EZH2Y646X. Our results indicate that EZH2Y646X alters the topology and function of chromatin domains to promote synergistic oncogenic programs.
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Affiliation(s)
- Maria C Donaldson-Collier
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stephanie Sungalee
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marie Zufferey
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elena Battistello
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Marco Mina
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kyle M Douglass
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Timo Rey
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Franck Raynaud
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Suliana Manley
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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24
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Maintenance of epigenetic landscape requires CIZ1 and is corrupted in differentiated fibroblasts in long-term culture. Nat Commun 2019; 10:460. [PMID: 30692537 PMCID: PMC6484225 DOI: 10.1038/s41467-018-08072-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/04/2018] [Indexed: 01/09/2023] Open
Abstract
The inactive X chromosome (Xi) serves as a model for establishment and maintenance of repressed chromatin and the function of polycomb repressive complexes (PRC1/2). Here we show that Xi transiently relocates from the nuclear periphery towards the interior during its replication, in a process dependent on CIZ1. Compromised relocation of Xi in CIZ1-null primary mouse embryonic fibroblasts is accompanied by loss of PRC-mediated H2AK119Ub1 and H3K27me3, increased solubility of PRC2 catalytic subunit EZH2, and genome-wide deregulation of polycomb-regulated genes. Xi position in S phase is also corrupted in cells adapted to long-term culture (WT or CIZ1-null), and also accompanied by specific changes in EZH2 and its targets. The data are consistent with the idea that chromatin relocation during S phase contributes to maintenance of epigenetic landscape in primary cells, and that elevated soluble EZH2 is part of an error-prone mechanism by which modifying enzyme meets template when chromatin relocation is compromised. The inactive X chromosome (Xi) is a model for establishment and maintenance of repressed chromatin and the function of polycomb repressive complexes. Here the authors show that Xi transiently relocates from the nuclear periphery during replication in a CIZ1-dependent manner, which plays a role in maintaining PRC-mediated repressed chromatin.
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25
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Bhatia V, Yadav A, Tiwari R, Nigam S, Goel S, Carskadon S, Gupta N, Goel A, Palanisamy N, Ateeq B. Epigenetic Silencing of miRNA-338-5p and miRNA-421 Drives SPINK1-Positive Prostate Cancer. Clin Cancer Res 2018; 25:2755-2768. [PMID: 30587549 DOI: 10.1158/1078-0432.ccr-18-3230] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/09/2018] [Accepted: 12/19/2018] [Indexed: 01/03/2023]
Abstract
PURPOSE Serine peptidase inhibitor, Kazal type-1 (SPINK1) overexpression defines the second most recurrent and aggressive prostate cancer subtype. However, the underlying molecular mechanism and pathobiology of SPINK1 in prostate cancer remains largely unknown. EXPERIMENTAL DESIGN miRNA prediction tools were employed to examine the SPINK1-3'UTR for miRNA binding. Luciferase reporter assays were performed to confirm the SPINK1-3'UTR binding of shortlisted miR-338-5p/miR-421. Furthermore, miR-338-5p/-421-overexpressing cancer cells (SPINK1-positive) were evaluated for oncogenic properties using cell-based functional assays and a mouse xenograft model. Global gene expression profiling was performed to unravel the biological pathways altered by miR-338-5p/-421. IHC and RNA in situ hybridization were carried out on prostate cancer patients' tissue microarray for SPINK1 and EZH2 expression, respectively. Chromatin immunoprecipitation assay was performed to examine EZH2 occupancy on the miR-338-5p/-421-regulatory regions. Bisulfite sequencing and methylated DNA immunoprecipitation were performed on prostate cancer cell lines and patients' specimens. RESULTS We established a critical role of miRNA-338-5p/-421 in posttranscriptional regulation of SPINK1. Ectopic expression of miRNA-338-5p/-421 in SPINK1-positive cells abrogates oncogenic properties including cell-cycle progression, stemness, and drug resistance, and shows reduced tumor burden and distant metastases in a mouse model. Importantly, we show that patients with SPINK1-positive prostate cancer exhibit increased EZH2 expression, suggesting its role in epigenetic silencing of miRNA-338-5p/-421. Furthermore, presence of CpG dinucleotide DNA methylation marks on the regulatory regions of miR-338-5p/-421 in SPINK1-positive prostate cancer cells and patients' specimens confirms epigenetic silencing. CONCLUSIONS Our findings revealed that miRNA-338-5p/-421 are epigenetically silenced in SPINK1-positive prostate cancer, although restoring the expression of these miRNAs using epigenetic drugs or synthetic mimics could abrogate SPINK1-mediated oncogenesis.See related commentary by Bjartell, p. 2679.
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Affiliation(s)
- Vipul Bhatia
- Molecular Oncology Lab, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Anjali Yadav
- Molecular Oncology Lab, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Ritika Tiwari
- Molecular Oncology Lab, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Shivansh Nigam
- Molecular Oncology Lab, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Sakshi Goel
- Molecular Oncology Lab, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Shannon Carskadon
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, Michigan
| | - Nilesh Gupta
- Department of Pathology, Henry Ford Health System, Detroit, Michigan
| | - Apul Goel
- Department of Urology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Nallasivam Palanisamy
- Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, Michigan
| | - Bushra Ateeq
- Molecular Oncology Lab, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India.
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26
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Ferreira M, Verbinnen I, Fardilha M, Van Eynde A, Bollen M. The deletion of the protein phosphatase 1 regulator NIPP1 in testis causes hyperphosphorylation and degradation of the histone methyltransferase EZH2. J Biol Chem 2018; 293:18031-18039. [PMID: 30305391 DOI: 10.1074/jbc.ac118.005577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/25/2018] [Indexed: 12/15/2022] Open
Abstract
Germ cell proliferation is epigenetically controlled, mainly through DNA methylation and histone modifications. However, the pivotal epigenetic regulators of germ cell self-renewal and differentiation in postnatal testis are still poorly defined. The histone methyltransferase enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of Polycomb repressive complex 2, represses target genes through trimethylation of histone H3 at Lys-27 (H3K27me3), and interacts (in)directly with both protein phosphatase 1 (PP1) and nuclear inhibitor of PP1 (NIPP1). Here, we report that postnatal, testis-specific ablation of NIPP1 in mice results in loss of EZH2 and reduces H3K27me3 levels. Mechanistically, the NIPP1 deletion abrogated PP1-mediated EZH2 dephosphorylation at two cyclin-dependent kinase sites (Thr-345/487), thereby generating hyperphosphorylated EZH2, which is a substrate for proteolytic degradation. Accordingly, alanine mutation of these residues prolonged the half-life of EZH2 in male germ cells. Our study discloses a key role for the PP1:NIPP1 holoenzyme in stabilizing EZH2 and maintaining the H3K27me3 mark on genes that are important for germ cell development and spermatogenesis.
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Affiliation(s)
- Mónica Ferreira
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and; Institute for Research in Biomedicine (iBiMED), Health Sciences Department, University of Aveiro, 3810 Aveiro, Portugal
| | - Iris Verbinnen
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and
| | - Margarida Fardilha
- Institute for Research in Biomedicine (iBiMED), Health Sciences Department, University of Aveiro, 3810 Aveiro, Portugal
| | - Aleyde Van Eynde
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and.
| | - Mathieu Bollen
- From the Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium and.
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27
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Reinhart D, Damjanovic L, Castan A, Ernst W, Kunert R. Differential gene expression of a feed-spiked super-producing CHO cell line. J Biotechnol 2018; 285:23-37. [PMID: 30157452 DOI: 10.1016/j.jbiotec.2018.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/15/2018] [Accepted: 08/25/2018] [Indexed: 01/09/2023]
Abstract
Feed supplements are concentrated cell culture media that contain a variety of nutrients, which can be added during a bioprocess. During fed-batch cultivation, feed media are typically added to a growing cell culture to maximize cell and product concentrations. In this study, only a single shot of feed medium was added on day 0 to a basal cell culture medium and compared to non-supplemented basal medium (feed-spiked at day 0 versus control experiments) by cultivation of a recombinant mAb expressing CHO cell line in batch mode under controlled conditions in a bioreactor. Since the feed-spike at day 0 was based on existing medium components without introducing additional supplements, a desirable process with decreased complexity was generated. Unlike cells in basal medium, feed-spiked cultures reached almost 2× higher peak cell concentrations (10 × 106 c/mL vs. 18 × 106 c/mL) and 3× higher antibody concentrations (0.8 g/L vs. 2.4 g/L). Batch process time and the integral over the viable cell count were similar for both process types. Constantly high cell-specific production rates in feed-spiked cultures (70 pg/cell/day) compared to continuously declining rates in basal medium (from 70 to 10 pg/cell/day) were responsible for an overall 70% higher cell-specific production rate and the higher product concentrations. To associate gene expression patterns to different process proceedings, transcriptome analysis was performed using microarrays. Several transcripts that are involved with glutamine de novo synthesis and citric acid cycle were significantly upregulated on several days in feed-spiked cultures. The top identified gene ontology (GO) terms related well to cell cycle and primary metabolism, cellular division as well as nucleobase formation or regulation, which indicated a more active proliferative state for feed-spiked cultures. KEGG biochemical pathway analysis and Gene set enrichment analysis (GSEA) further confirmed these findings from a complementary perspective. Moreover, several interesting gene targets, which have not yet been associated with recombinant protein expression, were identified that related to a higher proliferative state, growth, protein synthesis, cell-size control, metabolism, cell survival as well as genes that are associated with the control of the mammalian target of rapamycin (mTOR) in feed-spiked cultures. Analysis of critical product quality attributes (i.e. glycosylation, charge variants and size distribution) showed that feed-spiking did not change antibody quality.
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Affiliation(s)
- David Reinhart
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
| | - Lukas Damjanovic
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
| | - Andreas Castan
- GE Healthcare Life Sciences AB, Björkgatan 30, 75184, Uppsala, Sweden.
| | - Wolfgang Ernst
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
| | - Renate Kunert
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
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28
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Gil RS, Vagnarelli P. Protein phosphatases in chromatin structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:90-101. [PMID: 30036566 PMCID: PMC6227384 DOI: 10.1016/j.bbamcr.2018.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/29/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022]
Abstract
Chromatin structure and dynamics are highly controlled and regulated processes that play an essential role in many aspects of cell biology. The chromatin transition stages and the factors that control this process are regulated by post-translation modifications, including phosphorylation. While the role of protein kinases in chromatin dynamics has been quite well studied, the nature and regulation of the counteracting phosphatases represent an emerging field but are still at their infancy. In this review we summarize the current literature on phosphatases involved in the regulation of chromatin structure and dynamics, with emphases on the major knowledge gaps that should require attention and more investigation.
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Affiliation(s)
- Raquel Sales Gil
- Colleges of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Paola Vagnarelli
- Colleges of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK.
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29
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Murthy T, Bluemn T, Gupta AK, Reimer M, Rao S, Pillai MM, Minella AC. Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin. J Biol Chem 2018; 293:10220-10234. [PMID: 29764937 DOI: 10.1074/jbc.ra118.001654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/11/2018] [Indexed: 11/06/2022] Open
Abstract
Splicing factor 3B1 (SF3B1) is a core splicing protein that stabilizes the interaction between the U2 snRNA and the branch point in the mRNA target during splicing. SF3B1 is heavily phosphorylated at its N terminus and a substrate of cyclin-dependent kinases (CDKs). Although SF3B1 phosphorylation coincides with splicing catalysis, the functional significance of SF3B1 phosphorylation is largely undefined. Here, we show that SF3B1 phosphorylation follows a dynamic pattern during cell cycle progression that depends on CDK activity. SF3B1 is known to interact with chromatin, and we found that SF3B1 maximally interacts with nucleosomes during G1/S and that this interaction requires CDK2 activity. In contrast, SF3B1 disassociates from nucleosomes at G2/M, coinciding with a peak in CDK1-mediated SF3B1 phosphorylation. Thus, CDK1 and CDK2 appear to have opposing roles in regulating SF3B1-nucleosome interactions. Importantly, these interactions were modified by the presence and phosphorylation status of linker histone H1, particularly the H1.4 isoform. Performing genome-wide analysis of SF3B1-chromatin binding in synchronized cells, we observed that SF3B1 preferentially bound exons. Differences in SF3B1 chromatin binding to specific sites, however, did not correlate with changes in RNA splicing, suggesting that the SF3B1-nucleosome interaction does not determine cell cycle-dependent changes to mRNA splicing. Our results define a cell cycle stage-specific interaction between SF3B1 and nucleosomes that is mediated by histone H1 and depends on SF3B1 phosphorylation. Importantly, this interaction does not seem to be related to SF3B1's splicing function and, rather, points toward its potential role as a chromatin modifier.
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Affiliation(s)
- Tushar Murthy
- From the Driskill Graduate Program, Northwestern University, Chicago, Illinois 60611
| | - Theresa Bluemn
- the Medical College of Wisconsin, Milwaukee, Wisconsin 53226.,the Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin 53201, and
| | - Abhishek K Gupta
- the Section of Hematology, Yale Cancer Center and Yale University School of Medicine, New Haven, Connecticut 06510
| | - Michael Reimer
- the Medical College of Wisconsin, Milwaukee, Wisconsin 53226.,the Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin 53201, and
| | - Sridhar Rao
- the Medical College of Wisconsin, Milwaukee, Wisconsin 53226.,the Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin 53201, and
| | - Manoj M Pillai
- the Section of Hematology, Yale Cancer Center and Yale University School of Medicine, New Haven, Connecticut 06510
| | - Alex C Minella
- the Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, Wisconsin 53201, and
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30
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Köhn M. Miklós Bodanszky Award Lecture: Advances in the selective targeting of protein phosphatase-1 and phosphatase-2A with peptides. J Pept Sci 2018; 23:749-756. [PMID: 28876538 PMCID: PMC5639349 DOI: 10.1002/psc.3033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/20/2017] [Accepted: 07/23/2017] [Indexed: 12/13/2022]
Abstract
Protein phosphatase-1 and phosphatase-2A are two ubiquitously expressed enzymes known to catalyze the majority of dephosphorylation reactions on serine and threonine inside cells. They play roles in most cellular processes and are tightly regulated by regulatory subunits in holoenzymes. Their misregulation and malfunction contribute to disease development and progression, such as in cancer, diabetes, viral infections, and neurological as well as heart diseases. Therefore, targeting these phosphatases for therapeutic use would be highly desirable; however, their complex regulation and high conservation of the active site have been major hurdles for selectively targeting them in the past. In the last decade, new approaches have been developed to overcome these hurdles and have strongly revived the field. I will focus here on peptide-based approaches, which contributed to showing that these phosphatases can be targeted selectively and aided in rethinking the design of selective phosphatase modulators. Finally, I will give a perspective on www.depod.org, the human dephosphorylation database, and how it can aid phosphatase modulator design. © 2017 The Authors. Journal of Peptide Science published by European Peptide Society and John Wiley & Sons Ltd.
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Affiliation(s)
- Maja Köhn
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
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31
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Gerber T, Willscher E, Loeffler-Wirth H, Hopp L, Schadendorf D, Schartl M, Anderegg U, Camp G, Treutlein B, Binder H, Kunz M. Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. Oncotarget 2018; 8:846-862. [PMID: 27903987 PMCID: PMC5352202 DOI: 10.18632/oncotarget.13666] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/12/2016] [Indexed: 01/21/2023] Open
Abstract
Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma. Gene expression modules had prognostic relevance when compared with gene expression data from published melanoma samples and patient survival data. We surveyed kinome expression patterns across sub-populations of the BRAF/NRAS wild type sample and found that CDK4 and CDK2 were consistently highly expressed in the majority of cells, suggesting that these kinases might be involved in melanoma progression. Treatment of cells with the CDK4 inhibitor palbociclib restricted cell proliferation to a similar, and in some cases greater, extent than MAPK inhibitors. Finally, we identified a low abundant sub-population in this sample that highly expressed a module containing ABC transporter ABCB5, surface markers CD271 and CD133, and multiple aldehyde dehydrogenases (ALDHs). Patient-derived cultures of the BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant metastases showed more homogeneous single-cell gene expression patterns with gene expression modules for proliferation and ABC transporters. Taken together, our results describe an intertumor and intratumor heterogeneity in melanoma short-term cultures which might be relevant for patient survival, and suggest promising targets for new treatment approaches in melanoma therapy.
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Affiliation(s)
- Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, 04103 Leipzig, Germany
| | - Edith Willscher
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Lydia Hopp
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Dirk Schadendorf
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, 45147 Essen, Germany
| | - Manfred Schartl
- Department of Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97080 Würzburg, Germany.,Institute for Advanced Study, 3572 Texas A&M University, College Station, Texas 77843-3572, USA
| | - Ulf Anderegg
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
| | - Gray Camp
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, 04103 Leipzig, Germany
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, 04103 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
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32
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Ler LD, Ghosh S, Chai X, Thike AA, Heng HL, Siew EY, Dey S, Koh LK, Lim JQ, Lim WK, Myint SS, Loh JL, Ong P, Sam XX, Huang D, Lim T, Tan PH, Nagarajan S, Cheng CWS, Ho H, Ng LG, Yuen J, Lin PH, Chuang CK, Chang YH, Weng WH, Rozen SG, Tan P, Creasy CL, Pang ST, McCabe MT, Poon SL, Teh BT. Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Sci Transl Med 2017; 9:9/378/eaai8312. [PMID: 28228601 DOI: 10.1126/scitranslmed.aai8312] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022]
Abstract
Trithorax-like group complex containing KDM6A acts antagonistically to Polycomb-repressive complex 2 (PRC2) containing EZH2 in maintaining the dynamics of the repression and activation of gene expression through H3K27 methylation. In urothelial bladder carcinoma, KDM6A (a H3K27 demethylase) is frequently mutated, but its functional consequences and therapeutic targetability remain unknown. About 70% of KDM6A mutations resulted in a total loss of expression and a consequent loss of demethylase function in this cancer type. Further transcriptome analysis found multiple deregulated pathways, especially PRC2/EZH2, in KDM6A-mutated urothelial bladder carcinoma. Chromatin immunoprecipitation sequencing analysis revealed enrichment of H3K27me3 at specific loci in KDM6A-null cells, including PRC2/EZH2 and their downstream targets. Consequently, we targeted EZH2 (an H3K27 methylase) and demonstrated that KDM6A-null urothelial bladder carcinoma cell lines were sensitive to EZH2 inhibition. Loss- and gain-of-function assays confirmed that cells with loss of KDM6A are vulnerable to EZH2. IGFBP3, a direct KDM6A/EZH2/H3K27me3 target, was up-regulated by EZH2 inhibition and contributed to the observed EZH2-dependent growth suppression in KDM6A-null cell lines. EZH2 inhibition delayed tumor onset in KDM6A-null cells and caused regression of KDM6A-null bladder tumors in both patient-derived and cell line xenograft models. In summary, our study demonstrates that inactivating mutations of KDM6A, which are common in urothelial bladder carcinoma, are potentially targetable by inhibiting EZH2.
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Affiliation(s)
- Lian Dee Ler
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, 28 Medical Drive, Singapore 117456, Singapore
| | - Sujoy Ghosh
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Xiaoran Chai
- Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Aye Aye Thike
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Hong Lee Heng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ee Yan Siew
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Sucharita Dey
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore
| | - Liang Kai Koh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jing Quan Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Weng Khong Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jia Liang Loh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Pauline Ong
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Xin Xiu Sam
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Dachuan Huang
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Tony Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Puay Hoon Tan
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sanjanaa Nagarajan
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | | | - Henry Ho
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Lay Guat Ng
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - John Yuen
- Department of Urology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore
| | - Po-Hung Lin
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Cheng-Keng Chuang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Ying-Hsu Chang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan
| | - Wen-Hui Weng
- Department of Chemical Engineering and Biotechnology and Graduate Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Steven G Rozen
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.,Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore 169610, Singapore.,Genome Institute of Singapore, 60 Biopolis Street Genome, Singapore 138672, Singapore
| | - Caretha L Creasy
- Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - See-Tong Pang
- Division of Urooncology, Department of Urology, Chang Gung University and Memorial Hospital at LinKou, TaoYuan, Taiwan.
| | - Michael T McCabe
- Cancer Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.
| | - Song Ling Poon
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. .,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore 169610, Singapore. .,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Centre for Life Sciences, Singapore 117456, Singapore.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, #07-18, Singapore 138673, Singapore
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PRC2-mediated repression of SMARCA2 predicts EZH2 inhibitor activity in SWI/SNF mutant tumors. Proc Natl Acad Sci U S A 2017; 114:12249-12254. [PMID: 29087303 DOI: 10.1073/pnas.1703966114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Subunits of the SWI/SNF chromatin remodeling complex are frequently mutated in human cancers leading to epigenetic dependencies that are therapeutically targetable. The dependency on the polycomb repressive complex (PRC2) and EZH2 represents one such vulnerability in tumors with mutations in the SWI/SNF complex subunit, SNF5; however, whether this vulnerability extends to other SWI/SNF subunit mutations is not well understood. Here we show that a subset of cancers harboring mutations in the SWI/SNF ATPase, SMARCA4, is sensitive to EZH2 inhibition. EZH2 inhibition results in a heterogenous phenotypic response characterized by senescence and/or apoptosis in different models, and also leads to tumor growth inhibition in vivo. Lower expression of the SMARCA2 paralog was associated with cellular sensitivity to EZH2 inhibition in SMARCA4 mutant cancer models, independent of tissue derivation. SMARCA2 is suppressed by PRC2 in sensitive models, and induced SMARCA2 expression can compensate for SMARCA4 and antagonize PRC2 targets. The induction of SMARCA2 in response to EZH2 inhibition is required for apoptosis, but not for growth arrest, through a mechanism involving the derepression of the lysomal protease cathepsin B. Expression of SMARCA2 also delineates EZH2 inhibitor sensitivity for other SWI/SNF complex subunit mutant tumors, including SNF5 and ARID1A mutant cancers. Our data support monitoring SMARCA2 expression as a predictive biomarker for EZH2-targeted therapies in the context of SWI/SNF mutant cancers.
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34
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The protein phosphatase 1 regulator NIPP1 is essential for mammalian spermatogenesis. Sci Rep 2017; 7:13364. [PMID: 29042623 PMCID: PMC5645368 DOI: 10.1038/s41598-017-13809-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/29/2017] [Indexed: 12/22/2022] Open
Abstract
NIPP1 is one of the major nuclear interactors of protein phosphatase PP1. The deletion of NIPP1 in mice is early embryonic lethal, which has precluded functional studies in adult tissues. Hence, we have generated an inducible NIPP1 knockout model using a tamoxifen-inducible Cre recombinase transgene. The inactivation of the NIPP1 encoding alleles (Ppp1r8) in adult mice occurred very efficiently in testis and resulted in a gradual loss of germ cells, culminating in a Sertoli-cell only phenotype. Before the overt development of this phenotype Ppp1r8−/− testis showed a decreased proliferation and survival capacity of cells of the spermatogenic lineage. A reduced proliferation was also detected after the tamoxifen-induced removal of NIPP1 from cultured testis slices and isolated germ cells enriched for undifferentiated spermatogonia, hinting at a testis-intrinsic defect. Consistent with the observed phenotype, RNA sequencing identified changes in the transcript levels of cell-cycle and apoptosis regulating genes in NIPP1-depleted testis. We conclude that NIPP1 is essential for mammalian spermatogenesis because it is indispensable for the proliferation and survival of progenitor germ cells, including (un)differentiated spermatogonia.
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35
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Shoucri BM, Martinez ES, Abreo TJ, Hung VT, Moosova Z, Shioda T, Blumberg B. Retinoid X Receptor Activation Alters the Chromatin Landscape To Commit Mesenchymal Stem Cells to the Adipose Lineage. Endocrinology 2017; 158:3109-3125. [PMID: 28977589 PMCID: PMC5659689 DOI: 10.1210/en.2017-00348] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/11/2017] [Indexed: 01/15/2023]
Abstract
Developmental exposure to environmental factors has been linked to obesity risk later in life. Nuclear receptors are molecular sensors that play critical roles during development and, as such, are prime candidates to explain the developmental programming of disease risk by environmental chemicals. We have previously characterized the obesogen tributyltin (TBT), which activates the nuclear receptors peroxisome proliferator-activated receptor γ (PPARγ) and retinoid X receptor (RXR) to increase adiposity in mice exposed in utero. Mesenchymal stem cells (MSCs) from these mice are biased toward the adipose lineage at the expense of the osteoblast lineage, and MSCs exposed to TBT in vitro are shunted toward the adipose fate in a PPARγ-dependent fashion. To address where in the adipogenic cascade TBT acts, we developed an in vitro commitment assay that permitted us to distinguish early commitment to the adipose lineage from subsequent differentiation. TBT and RXR activators (rexinoids) had potent effects in committing MSCs to the adipose lineage, whereas the strong PPARγ activator rosiglitazone was inactive. We show that activation of RXR is sufficient for adipogenic commitment and that rexinoids act through RXR to alter the transcriptome in a manner favoring adipogenic commitment. RXR activation alters expression of enhancer of zeste homolog 2 (EZH2) and modifies genome-wide histone 3 lysine 27 trimethylation (H3K27me3) in promoting adipose commitment and programming subsequent differentiation. These data offer insights into the roles of RXR and EZH2 in MSC lineage specification and shed light on how endocrine-disrupting chemicals such as TBT can reprogram stem cell fate.
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Affiliation(s)
- Bassem M. Shoucri
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697-2300
- Medical Scientist Training Program, University of California, Irvine, Irvine, California 92697
| | - Eric S. Martinez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697-2300
| | - Timothy J. Abreo
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697-2300
| | - Victor T. Hung
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697-2300
| | - Zdena Moosova
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697-2300
- Masaryk University, Faculty of Science, RECETOX, 625 00 Brno, Czech Republic
| | - Toshi Shioda
- Massachusetts General Hospital Center for Cancer Research and Harvard Medical School, Charlestown, Massachusetts 02129
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697-2300
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697
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36
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de Castro IJ, Amin HA, Vinciotti V, Vagnarelli P. Network of phosphatases and HDAC complexes at repressed chromatin. Cell Cycle 2017; 16:2011-2017. [PMID: 28910568 PMCID: PMC5731419 DOI: 10.1080/15384101.2017.1371883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Tight regulation of gene expression is achieved by a variety of protein complexes that selectively bind chromatin, modify it and change its transcription competency. Histone acetylases (HATs) and deacetylases (HDACs) play an important role in this process. They can generate transcriptionally active or inactive chromatin through the addition (HATs) or removal (HDACs) of acetyl groups on histones, respectively. Repo-Man is a Protein Phosphatase 1 targeting subunit that accumulates on chromosomes during mitotic exit and mediates the removal of mitotic histone H3 phosphorylations. It was shown recently that Repo-Man also regulates heterochromatin formation in interphase and that its depletion favours the switch between transcriptionally inactive and active chromatin, demonstrating that its role goes well beyond mitosis. Here, we provide the first link between a phosphatase and HDAC complexes. We show that genome-wide Repo-Man binding sites overlap with chromatin regions bound by members of the three HDAC complexes (Sin3a, NuRD and CoREST). We establish that members of the NuRD and Sin3a HDAC complexes interact with Repo-Man by mass spectrometry and that Repo-Man is in close proximity to SAP18 (Sin3a) in interphase as observed by the Proximity Ligation Assay. Altogether, these data suggest a mechanism by which Repo-Man/PP1 complex, via interactions with HDACs, could stabilise gene repression.
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Affiliation(s)
- I J de Castro
- a Research Institute for Environment Health and Societies, Department of Life Sciences , Brunel University London , London , UK
| | - H A Amin
- a Research Institute for Environment Health and Societies, Department of Life Sciences , Brunel University London , London , UK
| | - V Vinciotti
- b Research Institute for Environment Health and Societies, Department of Mathematics , Brunel University London , London , UK
| | - P Vagnarelli
- a Research Institute for Environment Health and Societies, Department of Life Sciences , Brunel University London , London , UK
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37
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Laporte AN, Poulin NM, Barrott JJ, Wang XQ, Lorzadeh A, Vander Werff R, Jones KB, Underhill TM, Nielsen TO. Death by HDAC Inhibition in Synovial Sarcoma Cells. Mol Cancer Ther 2017; 16:2656-2667. [PMID: 28878027 DOI: 10.1158/1535-7163.mct-17-0397] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 12/30/2022]
Abstract
Conventional cytotoxic therapies for synovial sarcoma provide limited benefit, and no drugs specifically targeting the causative SS18-SSX fusion oncoprotein are currently available. Histone deacetylase (HDAC) inhibition has been shown in previous studies to disrupt the synovial sarcoma oncoprotein complex, resulting in apoptosis. To understand the molecular effects of HDAC inhibition, RNA-seq transcriptome analysis was undertaken in six human synovial sarcoma cell lines. HDAC inhibition induced pathways of cell-cycle arrest, neuronal differentiation, and response to oxygen-containing species, effects also observed in other cancers treated with this class of drugs. More specific to synovial sarcoma, polycomb group targets were reactivated, including tumor suppressor CDKN2A, and proapoptotic transcriptional patterns were induced. Functional analyses revealed that ROS-mediated FOXO activation and proapoptotic factors BIK, BIM, and BMF were important to apoptosis induction following HDAC inhibition in synovial sarcoma. HDAC inhibitor pathway activation results in apoptosis and decreased tumor burden following a 7-day quisinostat treatment in the Ptenfl/fl;hSS2 mouse model of synovial sarcoma. This study provides mechanistic support for a particular susceptibility of synovial sarcoma to HDAC inhibition as a means of clinical treatment. Mol Cancer Ther; 16(12); 2656-67. ©2017 AACR.
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Affiliation(s)
- Aimée N Laporte
- Faculty of Medicine, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Neal M Poulin
- Faculty of Medicine, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jared J Barrott
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Xiu Qing Wang
- Faculty of Medicine, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alireza Lorzadeh
- Department of Microbiology and Immunology, Michael Smith Laboratories Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan Vander Werff
- Department of Cellular and Physiological Sciences, Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin B Jones
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - T Michael Underhill
- Department of Cellular and Physiological Sciences, Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Torsten O Nielsen
- Faculty of Medicine, Vancouver Coastal Health Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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38
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Liu C, Liu R, Zhang D, Deng Q, Liu B, Chao HP, Rycaj K, Takata Y, Lin K, Lu Y, Zhong Y, Krolewski J, Shen J, Tang DG. MicroRNA-141 suppresses prostate cancer stem cells and metastasis by targeting a cohort of pro-metastasis genes. Nat Commun 2017; 8:14270. [PMID: 28112170 PMCID: PMC5264244 DOI: 10.1038/ncomms14270] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 12/13/2016] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs play important roles in regulating tumour development, progression and metastasis. Here we show that one of the miR-200 family members, miR-141, is under-expressed in several prostate cancer (PCa) stem/progenitor cell populations in both xenograft and primary patient tumours. Enforced expression of miR-141 in CD44+ and bulk PCa cells inhibits cancer stem cell properties including holoclone and sphere formation, as well as invasion, and suppresses tumour regeneration and metastasis. Moreover, miR-141 expression enforces a strong epithelial phenotype with a partial loss of mesenchymal phenotype. Whole-genome RNA sequencing uncovers novel miR-141-regulated molecular targets in PCa cells including the Rho GTPase family members (for example, CDC42, CDC42EP3, RAC1 and ARPC5) and stem cell molecules CD44 and EZH2, all of which are validated as direct and functionally relevant targets of miR-141. Our results suggest that miR-141 employs multiple mechanisms to obstruct tumour growth and metastasis. MicroRNAs have important roles in regulating tumor development, progression and metastasis. Here, the authors demonstrate the tumor-suppressive functions of miRNA141 in prostate cancer stem cells mediated by directly targeting CD44, Rho GTPase protein family members, and EZH2.
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Affiliation(s)
- Can Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA.,Cancer Stem Cell Institute, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Ruifang Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA.,Cancer Stem Cell Institute, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Carlton and Elm Streets, Buffalo, New York 14263, USA
| | - Dingxiao Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Carlton and Elm Streets, Buffalo, New York 14263, USA
| | - Qu Deng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Carlton and Elm Streets, Buffalo, New York 14263, USA.,Department of Epigenetics and Molecular Carcinogenesis, Program in Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences (GSBS), Houston, Texas 77030, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA
| | - Hsueh-Ping Chao
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA.,Department of Epigenetics and Molecular Carcinogenesis, Program in Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences (GSBS), Houston, Texas 77030, USA
| | - Kiera Rycaj
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Carlton and Elm Streets, Buffalo, New York 14263, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA
| | - Yi Zhong
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA
| | - John Krolewski
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA
| | - Dean G Tang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Texas 78957, USA.,Cancer Stem Cell Institute, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Carlton and Elm Streets, Buffalo, New York 14263, USA
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39
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Nyer DB, Daer RM, Vargas D, Hom C, Haynes KA. Regulation of cancer epigenomes with a histone-binding synthetic transcription factor. NPJ Genom Med 2017; 2. [PMID: 28919981 PMCID: PMC5600530 DOI: 10.1038/s41525-016-0002-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin proteins have expanded the mammalian synthetic biology toolbox by enabling control of active and silenced states at endogenous genes. Others have reported synthetic proteins that bind DNA and regulate genes by altering chromatin marks, such as histone modifications. Previously, we reported the first synthetic transcriptional activator, the "Polycomb-based transcription factor" (PcTF) that reads histone modifications through a protein-protein interaction between the polycomb chromodomain motif and trimethylated lysine 27 of histone H3 (H3K27me3). Here, we describe the genome-wide behavior of the polycomb-based transcription factor fusion protein. Transcriptome and chromatin profiling revealed several polycomb-based transcription factor-sensitive promoter regions marked by distal H3K27me3 and proximal fusion protein binding. These results illuminate a mechanism in which polycomb-based transcription factor interactions bridge epigenomic marks with the transcription initiation complex at target genes. In three cancer-derived human cell lines tested here, some target genes encode developmental regulators and tumor suppressors. Thus, the polycomb-based transcription factor represents a powerful new fusion protein-based method for cancer research and treatment where silencing marks are translated into direct gene activation.
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Affiliation(s)
- David B Nyer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Rene M Daer
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Daniel Vargas
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Caroline Hom
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 E Tyler Mall, Box 9709, Tempe, AZ 85287, USA
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40
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Huang Y, Tao Y, Hu K, Lin F, Li X, Feng T, Wang ZM. Hypoxia-induced NIPP1 activation enhances metastatic potential and predicts poor prognosis in hepatocellular carcinoma. Tumour Biol 2016; 37:14903-14914. [PMID: 27644248 DOI: 10.1007/s13277-016-5392-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/09/2016] [Indexed: 01/27/2023] Open
Abstract
Hypoxia is known to promote hepatocellular carcinoma (HCC) invasion and metastasis and nuclear inhibitor of protein phosphatase 1 (NIPP1) overexpression contributes to the malignant phenotype in HCC. The aim of this study was to investigate the role of NIPP1 in HCC development under hypoxia. We first conducted a study with 106 cases to explore the association of NIPP1 and/or enhancer of zeste homolog 2 (EZH2) expression with poor prognosis in HCC. Then additional 352 independent cases were recruited to validate the results in the first stage. Hypoxia was induced by culturing HCC cells in 1 % O2 or of the treatment with hypoxic agent. The expression levels of NIPP1/EZH2 in both HCC tissues and HCC cell lines were detected by RT-PCR, Western blot, or immunohistochemistry. We also studied the effects of the loss of function of NIPP1 and EZH2 on malignant phenotypes, downstream pathway, and inflammatory factors activities using gene silencing strategy. Overall, we found that NIPP1 and EZH2 were overexpressed in both HCC tissue samples and HCC cell lines. High expression of HIPP1 was associated with poor prognosis and clinicopathological features in patients with advanced HCC. HIPP1 expression positively correlated with the expression of hypoxia marker (carbonic anhydrase IX). Hypoxia induced high expression of NIPP1. NIPP1/EZH2 knockdown in HCC cell lines under hypoxia suppressed the malignant phenotypes, reduced the expression of hypoxia-inducible Factor 1α, downstream molecules of EZH2, and inhibit the activity of inflammatory factors. In conclusion, we found that NIPP1 could be activated by hypoxia and contributed to hypoxia-induced invasive and metastatic potential in HCC.
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Affiliation(s)
- Yun Huang
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410078, China
| | - Yiming Tao
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410078, China
| | - Kuan Hu
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410078, China
| | - Feng Lin
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410078, China
| | - Xinying Li
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410078, China
| | - Tiecheng Feng
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410078, China
| | - Zhi-Ming Wang
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410078, China.
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Epstein-Barr Virus Oncoprotein LMP1 Mediates Epigenetic Changes in Host Gene Expression through PARP1. J Virol 2016; 90:8520-30. [PMID: 27440880 DOI: 10.1128/jvi.01180-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/11/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED The latent infection of Epstein-Barr virus (EBV) is associated with 1% of human cancer incidence. Poly(ADP-ribosyl)ation (PARylation) is a posttranslational modification catalyzed by poly(ADP-ribose) polymerases (PARPs) that mediate EBV replication during latency. In this study, we detail the mechanisms that drive cellular PARylation during latent EBV infection and the effects of PARylation on host gene expression and cellular function. EBV-infected B cells had higher PAR levels than EBV-negative B cells. Moreover, cellular PAR levels were up to 2-fold greater in type III than type I latently infected EBV B cells. We identified a positive association between expression of the EBV genome-encoded latency membrane protein 1 (LMP1) and PAR levels that was dependent upon PARP1. PARP1 regulates gene expression by numerous mechanisms, including modifying chromatin structure and altering the function of chromatin-modifying enzymes. Since LMP1 is essential in establishing EBV latency and promoting tumorigenesis, we explored the model that disruption in cellular PARylation, driven by LMP1 expression, subsequently promotes epigenetic alterations to elicit changes in host gene expression. PARP1 inhibition resulted in the accumulation of the repressive histone mark H3K27me3 at a subset of LMP1-regulated genes. Inhibition of PARP1, or abrogation of PARP1 expression, also suppressed the expression of LMP1-activated genes and LMP1-mediated cellular transformation, demonstrating an essential role for PARP1 activity in LMP1-induced gene expression and cellular transformation associated with LMP1. In summary, we identified a novel mechanism by which LMP1 drives expression of host tumor-promoting genes by blocking generation of the inhibitory histone modification H3K27me3 through PARP1 activation. IMPORTANCE EBV is causally linked to several malignancies and is responsible for 1% of cancer incidence worldwide. The EBV-encoded protein LMP1 is essential for promoting viral tumorigenesis by aberrant activation of several well-known intracellular signaling pathways. We have identified and defined an additional novel molecular mechanism by which LMP1 regulates the expression of tumor-promoting host genes. We found that LMP1 activates the cellular protein PARP1, leading to a decrease in a repressive histone modification, accompanied by induction in expression of multiple cancer-related genes. PARP1 inhibition or depletion led to a decrease in LMP1-induced cellular transformation. Therefore, targeting PARP1 activity may be an effective treatment for EBV-associated malignancies.
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Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma. Blood 2016; 128:1234-45. [PMID: 27297792 DOI: 10.1182/blood-2016-03-707141] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/25/2016] [Indexed: 12/15/2022] Open
Abstract
Peripheral T-cell lymphomas (PTCLs) represent a heterogeneous group of T-cell malignancies that generally demonstrate aggressive clinical behavior, often are refractory to standard therapy, and remain significantly understudied. The most common World Health Organization subtype is PTCL, not otherwise specified (NOS), essentially a "wastebasket" category because of inadequate understanding to assign cases to a more specific diagnostic entity. Identification of novel fusion genes has contributed significantly to improving the classification, biologic understanding, and therapeutic targeting of PTCLs. Here, we integrated mate-pair DNA and RNA next-generation sequencing to identify chromosomal rearrangements encoding expressed fusion transcripts in PTCL, NOS. Two of 11 cases had novel fusions involving VAV1, encoding a truncated form of the VAV1 guanine nucleotide exchange factor important in T-cell receptor signaling. Fluorescence in situ hybridization studies identified VAV1 rearrangements in 10 of 148 PTCLs (7%). These were observed exclusively in PTCL, NOS (11%) and anaplastic large cell lymphoma (11%). In vitro, ectopic expression of a VAV1 fusion promoted cell growth and migration in a RAC1-dependent manner. This growth was inhibited by azathioprine, a clinically available RAC1 inhibitor. We also identified novel kinase gene fusions, ITK-FER and IKZF2-ERBB4, as candidate therapeutic targets that show similarities to known recurrent oncogenic ITK-SYK fusions and ERBB4 transcript variants in PTCLs, respectively. Additional novel and potentially clinically relevant fusions also were discovered. Together, these findings identify VAV1 fusions as recurrent and targetable events in PTCLs and highlight the potential for clinical sequencing to guide individualized therapy approaches for this group of aggressive malignancies.
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Lopez G, Song Y, Lam R, Ruder D, Creighton CJ, Bid HK, Bill KL, Bolshakov S, Zhang X, Lev D, Pollock RE. HDAC Inhibition for the Treatment of Epithelioid Sarcoma: Novel Cross Talk Between Epigenetic Components. Mol Cancer Res 2015; 14:35-43. [PMID: 26396249 DOI: 10.1158/1541-7786.mcr-15-0295] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/11/2015] [Indexed: 01/22/2023]
Abstract
UNLABELLED Epithelioid sarcoma is a rare neoplasm uniquely comprised of cells exhibiting both mesenchymal and epithelial features. Having propensity for local and distant recurrence, it poses a diagnostic dilemma secondary to pathologic complexity. Patients have dismal prognosis due to lack of effective therapy. HDAC inhibitors (HDACi) exhibit marked antitumor effects in various malignancies. The studies here demonstrate that pan-HDAC inhibitors constitute novel therapeutics versus epithelioid sarcoma. Human ES cells (VAESBJ, HS-ES, Epi-544) were studied in preclinical models to evaluate HDACi effects. Immunoblot and RT-PCR were used to evaluate expression of acetylated tubulin, histones H3/H4, EZH2 upon HDACi. MTS and clonogenic assays were used to assess the impact of HDACi on cell growth. Cell culture assays were used to evaluate the impact of HDACi and EZH2-specific siRNA inhibition on cell-cycle progression and survival. Unbiased gene array analysis was used to identify the impact of HDACi on epithelioid sarcoma gene expression. Xenografts were used to evaluate epithelioid sarcoma tumor growth in response to HDACi. HDAC inhibition increased target protein acetylation and abrogated cell growth and colony formation in epithelioid sarcoma cells. HDACi induced G(2) cell-cycle arrest and marked apoptosis, and reduced tumor growth in xenograft models. HDACi induced widespread gene expression changes, and EZH2 was significantly downregulated. EZH2 knockdown resulted in abrogated cell growth in vitro. IMPLICATIONS The current study suggests a clinical role for HDACi in human epithelioid sarcoma, which, when combined with EZH2 inhibitors, could serve as a novel therapeutic strategy for epithelioid sarcoma patients. Future investigations targeting specific HDAC isoforms along with EZH2 may potentially maximizing treatment efficacy.
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Affiliation(s)
- Gonzalo Lopez
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Yechun Song
- Department of Neurosurgery, Guiyang 300 Hospital, Zunyi Medical College, Guizhou, China
| | - Ryan Lam
- GRU-UGA Medical Partnership, Georgia Regents University, Athens, Georgia
| | - Dennis Ruder
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, Texas
| | - Chad J Creighton
- Department of Medicine and Dan L. Duncan Division of Biostatistics, Baylor College of Medicine, Houston, Texas. Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, Texas
| | - Hemant Kumar Bid
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Kate Lynn Bill
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Svetlana Bolshakov
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, Texas
| | - Xiaoli Zhang
- Center for Biostatistics, The Ohio State University, Columbus, Ohio
| | - Dina Lev
- Surgery B, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
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Global Transcriptome Analysis Reveals That Poly(ADP-Ribose) Polymerase 1 Regulates Gene Expression through EZH2. Mol Cell Biol 2015; 35:3934-44. [PMID: 26370511 DOI: 10.1128/mcb.00635-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/08/2015] [Indexed: 11/20/2022] Open
Abstract
Posttranslational modifications, such as poly(ADP-ribosyl)ation (PARylation), regulate chromatin-modifying enzymes, ultimately affecting gene expression. This study explores the role of poly(ADP-ribose) polymerase (PARP) on global gene expression in a lymphoblastoid B cell line. We found that inhibition of PARP catalytic activity with olaparib resulted in global gene deregulation, affecting approximately 11% of the genes expressed. Gene ontology analysis revealed that PARP could exert these effects through transcription factors and chromatin-remodeling enzymes, including the polycomb repressive complex 2 (PRC2) member EZH2. EZH2 mediates the trimethylation of histone H3 at lysine 27 (H3K27me3), a modification associated with chromatin compaction and gene silencing. Both pharmacological inhibition of PARP and knockdown of PARP1 induced the expression of EZH2, which resulted in increased global H3K27me3. Chromatin immunoprecipitation confirmed that PARP1 inhibition led to H3K27me3 deposition at EZH2 target genes, which resulted in gene silencing. Moreover, increased EZH2 expression is attributed to the loss of the occupancy of the transcription repressor E2F4 at the EZH2 promoter following PARP inhibition. Together, these data show that PARP plays an important role in global gene regulation and identifies for the first time a direct role of PARP1 in regulating the expression and function of EZH2.
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Gindin Y, Jiang Y, Francis P, Walker RL, Abaan OD, Zhu YJ, Meltzer PS. miR-23a impairs bone differentiation in osteosarcoma via down-regulation of GJA1. Front Genet 2015; 6:233. [PMID: 26191074 PMCID: PMC4488756 DOI: 10.3389/fgene.2015.00233] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/18/2015] [Indexed: 01/04/2023] Open
Abstract
Osteosarcoma is the most common type of bone cancer in children and adolescents. Impaired differentiation of osteoblast cells is a distinguishing feature of this aggressive disease. As improvements in survival outcomes have largely plateaued, better understanding of the bone differentiation program may provide new treatment approaches. The miRNA cluster miR-23a~27a~24-2, particularly miR-23a, has been shown to interact with genes important for bone development. However, global changes in gene expression associated with functional gain of this cluster have not been fully explored. To better understand the relationship between miR-23a expression and bone cell differentiation, we carried out a large-scale gene expression analysis in HOS cells. Experimental results demonstrate that over-expression of miR-23a delays differentiation in this system. Downstream bioinformatic analysis identified miR-23a target gene connexin-43 (Cx43/GJA1), a mediator of intercellular signaling critical to osteoblast development, as acutely affected by miR-23a levels. Connexin-43 is up-regulated in the course of HOS cell differentiation and is down-regulated in cells transfected with miR-23a. Analysis of gene expression data, housed at Gene Expression Omnibus, reveals that Cx43 is consistently up-regulated during osteoblast differentiation. Suppression of Cx43 mRNA by miR-23a was confirmed in vitro using a luciferase reporter assay. This work demonstrates novel interactions between microRNA expression, intercellular signaling and bone differentiation in osteosarcoma.
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Affiliation(s)
- Yevgeniy Gindin
- Genetics Branch, Center for Cancer Research, National Institutes of Health Bethesda, MD, USA ; Graduate Program in Bioinformatics, Boston University Boston, MA, USA
| | - Yuan Jiang
- Genetics Branch, Center for Cancer Research, National Institutes of Health Bethesda, MD, USA
| | - Princy Francis
- Genetics Branch, Center for Cancer Research, National Institutes of Health Bethesda, MD, USA
| | - Robert L Walker
- Genetics Branch, Center for Cancer Research, National Institutes of Health Bethesda, MD, USA
| | - Ogan D Abaan
- Genetics Branch, Center for Cancer Research, National Institutes of Health Bethesda, MD, USA
| | - Yuelin J Zhu
- Genetics Branch, Center for Cancer Research, National Institutes of Health Bethesda, MD, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Institutes of Health Bethesda, MD, USA
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Liu C, Li S, Dai X, Ma J, Wan J, Jiang H, Wang P, Liu Z, Zhang H. PRC2 regulates RNA polymerase III transcribed non-translated RNA gene transcription through EZH2 and SUZ12 interaction with TFIIIC complex. Nucleic Acids Res 2015; 43:6270-84. [PMID: 26038315 PMCID: PMC4513857 DOI: 10.1093/nar/gkv574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/20/2015] [Indexed: 11/12/2022] Open
Abstract
Polycomb repression complex 2 (PRC2) component EZH2 tri-methylates H3K27 and exerts epigenetic repression on target gene expression. EZH2-mediated epigenetic control of RNA polymerase II (Pol II) transcribed coding gene transcription has been well established. However, little is known about EZH2-mediated epigenetic regulation of RNA polymerase III (Pol III) transcription. Here we present a paradigm that EZH2 is involved in the repression of Pol III transcription via interaction with transcriptional factor complex IIIC (TFIIIC). EZH2 and H3K27me3 co-occupy the promoter of tRNATyr, 5S rRNA and 7SL RNA genes. Depletion of EZH2 or inhibition of EZH2 methyltransferase activity led to upregulation of Pol III target gene transcription. EZH2-mediated repression of Pol III transcribed gene expression requires presence of SUZ12. SUZ12 was able to interact with TFIIIC complex and knockdown of SUZ12 decreased occupancy of EZH2 and H3K27me3 at the promoter of Pol III target genes. Our findings pointed out a previously unidentified role of PRC2 complex in suppressing transcription of Pol III transcribed non-translated RNA genes, putting Pol III on a new layer of epigenetic regulation.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Shuai Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Xiaoyan Dai
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Ji Ma
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Junhu Wan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hao Jiang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Peng Wang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Zhaoli Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
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Yang XH, Wang B, Cunningham JM. Identification of epigenetic modifications that contribute to pathogenesis in therapy-related AML: Effective integration of genome-wide histone modification with transcriptional profiles. BMC Med Genomics 2015; 8 Suppl 2:S6. [PMID: 26043758 PMCID: PMC4460748 DOI: 10.1186/1755-8794-8-s2-s6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Therapy-related, secondary acute myeloid leukemia (t-AML) is an increasingly frequent complication of intensive chemotherapy. This malignancy is often characterized by abnormalities of chromosome 7, including large deletions or chromosomal loss. A variety of studies suggest that decreased expression of the EZH2 gene located at 7q36.1 is critical in disease pathogenesis. This histone methyltransferase has been implicated in transcriptional repression through modifying histone H3 on lysine 27 (H3k27). However, the critical target genes of EZH2 and their regulatory roles remain unclear. Method To characterize the subset of EZH2 target genes that might contribute to t-AML pathogenesis, we developed a novel computational analysis to integrate tissue-specific histone modifications and genome-wide transcriptional regulation. Initial integrative analysis utilized a novel "seq2gene" strategy to explore largely the target genes of chromatin immuneprecipitation sequencing (ChIP-seq) enriched regions. By combining seq2gene with our Phenotype-Genotype-Network (PGNet) algorithm, we enriched genes with similar expression profiles and genomic or functional characteristics into "biomodules". Results Initial studies identified SEMA3A (semaphoring 3A) as a novel oncogenic candidate that is regulated by EZH2-silencing, using data derived from both normal and leukemic cell lines as well as murine cells deficient in EZH2. A microsatellite marker at the SEMA3A promoter has been associated with chemosensitivity and radiosensitivity. Notably, our subsequent studies in primary t-AML demonstrate an expected up-regulation of SEMA3A that is EZH2-modulated. Furthermore, we have identified three biomodules that are co-expressed with SEMA3A and up-regulated in t-AML, one of which consists of previously characterized EZH2-repressed gene targets. The other two biomodules include MAPK8 and TATA box targets. Together, our studies suggest an important role for EZH2 targets in t-AML pathogenesis that warrants further study. Conclusion These developed computational algorithms and systems biology strategies will enhance the knowledge discovery and hypothesis-driven analysis of multiple next generation sequencing data, for t-AML and other complex diseases.
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Verheyen T, Görnemann J, Verbinnen I, Boens S, Beullens M, Van Eynde A, Bollen M. Genome-wide promoter binding profiling of protein phosphatase-1 and its major nuclear targeting subunits. Nucleic Acids Res 2015; 43:5771-84. [PMID: 25990731 PMCID: PMC4499128 DOI: 10.1093/nar/gkv500] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/05/2015] [Indexed: 12/11/2022] Open
Abstract
Protein phosphatase-1 (PP1) is a key regulator of transcription and is targeted to promoter regions via associated proteins. However, the chromatin binding sites of PP1 have never been studied in a systematic and genome-wide manner. Methylation-based DamID profiling in HeLa cells has enabled us to map hundreds of promoter binding sites of PP1 and three of its major nuclear interactors, i.e. RepoMan, NIPP1 and PNUTS. Our data reveal that the α, β and γ isoforms of PP1 largely bind to distinct subsets of promoters and can also be differentiated by their promoter binding pattern. PP1β emerged as the major promoter-associated isoform and shows an overlapping binding profile with PNUTS at dozens of active promoters. Surprisingly, most promoter binding sites of PP1 are not shared with RepoMan, NIPP1 or PNUTS, hinting at the existence of additional, largely unidentified chromatin-targeting subunits. We also found that PP1 is not required for the global chromatin targeting of RepoMan, NIPP1 and PNUTS, but alters the promoter binding specificity of NIPP1. Our data disclose an unexpected specificity and complexity in the promoter binding of PP1 isoforms and their chromatin-targeting subunits.
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Affiliation(s)
- Toon Verheyen
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Janina Görnemann
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Iris Verbinnen
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Shannah Boens
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Monique Beullens
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Aleyde Van Eynde
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
| | - Mathieu Bollen
- Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, B-3000 Leuven, Belgium
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Protein phosphatase PP1-NIPP1 activates mesenchymal genes in HeLa cells. FEBS Lett 2015; 589:1314-21. [DOI: 10.1016/j.febslet.2015.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 11/22/2022]
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50
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Luzhna L, Kutanzi K, Kovalchuk O. Gene expression and epigenetic profiles of mammary gland tissue: Insight into the differential predisposition of four rat strains to mammary gland cancer. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 779:39-56. [DOI: 10.1016/j.mrgentox.2014.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 12/29/2022]
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