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Ramanarayanan V, Oberdoerffer P. AKTing on R Loops Makes for an ATRactive Target in Ovarian Cancer Therapy. Cancer Res 2024; 84:793-795. [PMID: 38486481 DOI: 10.1158/0008-5472.can-23-4129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 03/19/2024]
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the deadliest subtype of ovarian cancer. While PARP inhibitors (PARPi) have transformed the care of advanced HGSOC, PARPi resistance poses a major limitation to their clinical utility. DNA damage checkpoint signaling via ATR kinase can counteract PARPi-induced replication stress, making ATR an attractive therapeutic target in PARPi-resistant tumors. However, ATR inhibitor (ATRi) efficacy in the clinic is low, emphasizing the need for suitable combination treatments. In this issue of Cancer Research, Huang and colleagues uncovered cytotoxic synergism between inhibition of the PI3K/AKT pathway and ATR based on high-throughput screening for ATRi drug combinations in PARPi-resistant HGSOC cells. Dual inhibition of ATR and AKT resulted in aberrant replication stress and cell death, which was attributed in part to impaired resolution of replication-stalling RNA:DNA hybrids (R loops). The authors identified the DNA/RNA helicase DHX9 as a clinically relevant candidate effector of R loop resolution in HGSOC. AKT interacted with and recruited DHX9 to R loops, where it complemented ATR in facilitating their removal. Underlining the therapeutic potential relevance of these findings, combined inhibition of ATR and AKT caused near complete tumor regression in HGSOC xenograft models, and elevated AKT/DHX9 levels correlated with poor survival in patients with HGSOC. Of note, the genotoxic consequences of dual ATRi/AKTi treatment extended beyond PARPi-resistant tumors and are likely to affect genome integrity beyond R loops. The work by Huang and colleagues thus provides compelling rationale for the exploration of combined targeting of the AKT and ATR pathways as a potentially broadly applicable treatment of advanced HGSOC. See related article by Huang et al., p. 887.
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Affiliation(s)
- Vijayalalitha Ramanarayanan
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Philipp Oberdoerffer
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
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2
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Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, Salfati EL, Blanchette M, Munding EM, Bhakta M, Chew YC, Guo W, Yang X, Maybury-Lewis S, Tian X, Ross JM, Coppotelli G, Meer MV, Rogers-Hammond R, Vera DL, Lu YR, Pippin JW, Creswell ML, Dou Z, Xu C, Mitchell SJ, Das A, O'Connell BL, Thakur S, Kane AE, Su Q, Mohri Y, Nishimura EK, Schaevitz L, Garg N, Balta AM, Rego MA, Gregory-Ksander M, Jakobs TC, Zhong L, Wakimoto H, El Andari J, Grimm D, Mostoslavsky R, Wagers AJ, Tsubota K, Bonasera SJ, Palmeira CM, Seidman JG, Seidman CE, Wolf NS, Kreiling JA, Sedivy JM, Murphy GF, Green RE, Garcia BA, Berger SL, Oberdoerffer P, Shankland SJ, Gladyshev VN, Ksander BR, Pfenning AR, Rajman LA, Sinclair DA. Loss of epigenetic information as a cause of mammalian aging. Cell 2024; 187:1312-1313. [PMID: 38428398 DOI: 10.1016/j.cell.2024.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
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3
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Soutoglou E, Oberdoerffer P. Maintenance of genome integrity under physical constraints. Chromosoma 2024; 133:1-3. [PMID: 38355990 DOI: 10.1007/s00412-024-00816-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Affiliation(s)
- Evi Soutoglou
- Genome Damage and Stability Centre, Sussex University, School of Life Sciences, University of Sussex, Brighton, BN1 9RH, UK.
| | - Philipp Oberdoerffer
- Department of Radiation Oncology & Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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4
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Yu ZC, Li T, Tully E, Huang P, Chen CN, Oberdoerffer P, Gaillard S, Shih IM, Wang TL. Temozolomide Sensitizes ARID1A-Mutated Cancers to PARP Inhibitors. Cancer Res 2023; 83:2750-2762. [PMID: 37306706 PMCID: PMC10527942 DOI: 10.1158/0008-5472.can-22-3646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/02/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
ARID1A is a subunit of SWI/SNF chromatin remodeling complexes and is mutated in many types of human cancers, especially those derived from endometrial epithelium, including ovarian and uterine clear cell carcinoma (CCC) and endometrioid carcinoma (EMCA). Loss-of-function mutations in ARID1A alter epigenetic regulation of transcription, cell-cycle checkpoint control, and DNA damage repair. We report here that mammalian cells with ARID1A deficiency harbor accumulated DNA base lesions and increased abasic (AP) sites, products of glycosylase in the first step of base excision repair (BER). ARID1A mutations also delayed recruitment kinetics of BER long-patch repair effectors. Although ARID1A-deficient tumors were not sensitive to monotherapy with DNA-methylating temozolomide (TMZ), the combination of TMZ with PARP inhibitors (PARPi) potently elicited double-strand DNA breaks, replication stress, and replication fork instability in ARID1A-deficient cells. The TMZ and PARPi combination also significantly delayed in vivo growth of ovarian tumor xenografts carrying ARID1A mutations and induced apoptosis and replication stress in xenograft tumors. Together, these findings identified a synthetic lethal strategy to enhance the response of ARID1A-mutated cancers to PARP inhibition, which warrants further experimental exploration and clinical trial validation. SIGNIFICANCE The combination of temozolomide and PARP inhibitor exploits the specific DNA damage repair status of ARID1A-inactivated ovarian cancers to suppress tumor growth.
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Affiliation(s)
- Zheng-Cheng Yu
- Departments of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Tianhe Li
- Departments of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Ellen Tully
- Departments of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Peng Huang
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Chih-Ning Chen
- Departments of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Philipp Oberdoerffer
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Radiation Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Stephanie Gaillard
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Ie-Ming Shih
- Departments of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
| | - Tian-Li Wang
- Departments of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
- Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD, 21231, USA
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5
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Oberdoerffer P, Miller KM. Histone H2A variants: Diversifying chromatin to ensure genome integrity. Semin Cell Dev Biol 2023; 135:59-72. [PMID: 35331626 PMCID: PMC9489817 DOI: 10.1016/j.semcdb.2022.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Histone variants represent chromatin components that diversify the structure and function of the genome. The variants of H2A, primarily H2A.X, H2A.Z and macroH2A, are well-established participants in DNA damage response (DDR) pathways, which function to protect the integrity of the genome. Through their deposition, post-translational modifications and unique protein interaction networks, these variants guard DNA from endogenous threats including replication stress and genome fragility as well as from DNA lesions inflicted by exogenous sources. A growing body of work is now providing a clearer picture on the involvement and mechanistic basis of H2A variant contribution to genome integrity. Beyond their well-documented role in gene regulation, we review here how histone H2A variants promote genome stability and how alterations in these pathways contribute to human diseases including cancer.
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Affiliation(s)
- Philipp Oberdoerffer
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, Salfati EL, Blanchette M, Munding EM, Bhakta M, Chew YC, Guo W, Yang X, Maybury-Lewis S, Tian X, Ross JM, Coppotelli G, Meer MV, Rogers-Hammond R, Vera DL, Lu YR, Pippin JW, Creswell ML, Dou Z, Xu C, Mitchell SJ, Das A, O'Connell BL, Thakur S, Kane AE, Su Q, Mohri Y, Nishimura EK, Schaevitz L, Garg N, Balta AM, Rego MA, Gregory-Ksander M, Jakobs TC, Zhong L, Wakimoto H, El Andari J, Grimm D, Mostoslavsky R, Wagers AJ, Tsubota K, Bonasera SJ, Palmeira CM, Seidman JG, Seidman CE, Wolf NS, Kreiling JA, Sedivy JM, Murphy GF, Green RE, Garcia BA, Berger SL, Oberdoerffer P, Shankland SJ, Gladyshev VN, Ksander BR, Pfenning AR, Rajman LA, Sinclair DA. Loss of epigenetic information as a cause of mammalian aging. Cell 2023; 186:305-326.e27. [PMID: 36638792 PMCID: PMC10166133 DOI: 10.1016/j.cell.2022.12.027] [Citation(s) in RCA: 156] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 08/09/2022] [Accepted: 12/15/2022] [Indexed: 01/13/2023]
Abstract
All living things experience an increase in entropy, manifested as a loss of genetic and epigenetic information. In yeast, epigenetic information is lost over time due to the relocalization of chromatin-modifying proteins to DNA breaks, causing cells to lose their identity, a hallmark of yeast aging. Using a system called "ICE" (inducible changes to the epigenome), we find that the act of faithful DNA repair advances aging at physiological, cognitive, and molecular levels, including erosion of the epigenetic landscape, cellular exdifferentiation, senescence, and advancement of the DNA methylation clock, which can be reversed by OSK-mediated rejuvenation. These data are consistent with the information theory of aging, which states that a loss of epigenetic information is a reversible cause of aging.
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Affiliation(s)
- Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA.
| | - Motoshi Hayano
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Ophthalmology, Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Patrick T Griffin
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - João A Amorim
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Michael S Bonkowski
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - John K Apostolides
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Elias L Salfati
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | | | | | - Mital Bhakta
- Cantata/Dovetail Genomics, Scotts Valley, CA, USA
| | | | - Wei Guo
- Zymo Research Corporation, Irvine, CA, USA
| | | | - Sun Maybury-Lewis
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Jaime M Ross
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Giuseppe Coppotelli
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Margarita V Meer
- Department of Medicine, Brigham and Women's Hospital, HMS, Boston, MA, USA
| | - Ryan Rogers-Hammond
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Daniel L Vera
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Yuancheng Ryan Lu
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Jeffrey W Pippin
- Division of Nephrology, University of Washington, Seattle, WA, USA
| | - Michael L Creswell
- Division of Nephrology, University of Washington, Seattle, WA, USA; Georgetown University School of Medicine, Washington, DC, USA
| | - Zhixun Dou
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Caiyue Xu
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Abhirup Das
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Pharmacology, UNSW, Sydney, NSW, Australia
| | | | - Sachin Thakur
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Alice E Kane
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Qiao Su
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yasuaki Mohri
- Department of Stem Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Emi K Nishimura
- Department of Stem Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Neha Garg
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Ana-Maria Balta
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Meghan A Rego
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | | | - Tatjana C Jakobs
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, HMS, Boston, MA, USA
| | - Lei Zhong
- The Massachusetts General Hospital Cancer Center, HMS, Boston, MA, USA
| | | | - Jihad El Andari
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, BioQuant, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, BioQuant, Heidelberg, Germany
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, HMS, Boston, MA, USA
| | - Amy J Wagers
- Paul F. Glenn Center for Biology of Aging Research, Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Joslin Diabetes Center, Boston, MA, USA
| | - Kazuo Tsubota
- Department of Ophthalmology, Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Stephen J Bonasera
- Division of Geriatrics, University of Nebraska Medical Center, Durham Research Center II, Omaha, NE, USA
| | - Carlos M Palmeira
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | | | | | - Norman S Wolf
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Jill A Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - George F Murphy
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Richard E Green
- Department of Biomolecular Engineering, UCSC, Santa Cruz, CA, USA
| | - Benjamin A Garcia
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital, HMS, Boston, MA, USA
| | - Bruce R Ksander
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, HMS, Boston, MA, USA
| | - Andreas R Pfenning
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Luis A Rajman
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - David A Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA.
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7
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Sebastian R, Aladjem MI, Oberdoerffer P. Encounters in Three Dimensions: How Nuclear Topology Shapes Genome Integrity. Front Genet 2021; 12:746380. [PMID: 34745220 PMCID: PMC8566435 DOI: 10.3389/fgene.2021.746380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Almost 25 years ago, the phosphorylation of a chromatin component, histone H2AX, was discovered as an integral part of the DNA damage response in eukaryotes. Much has been learned since then about the control of DNA repair in the context of chromatin. Recent technical and computational advances in imaging, biophysics and deep sequencing have led to unprecedented insight into nuclear organization, highlighting the impact of three-dimensional (3D) chromatin structure and nuclear topology on DNA repair. In this review, we will describe how DNA repair processes have adjusted to and in many cases adopted these organizational features to ensure accurate lesion repair. We focus on new findings that highlight the importance of chromatin context, topologically associated domains, phase separation and DNA break mobility for the establishment of repair-conducive nuclear environments. Finally, we address the consequences of aberrant 3D genome maintenance for genome instability and disease.
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Affiliation(s)
- Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Philipp Oberdoerffer
- Division of Cancer Biology, National Cancer Institute, NIH, Rockville, MD, United States
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8
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Sebastian R, Hosogane EK, Sun EG, Tran AD, Reinhold WC, Burkett S, Sturgill DM, Gudla PR, Pommier Y, Aladjem MI, Oberdoerffer P. Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability. Mol Cell 2020; 79:836-845.e7. [PMID: 32649884 DOI: 10.1016/j.molcel.2020.06.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 04/24/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
The inactive X chromosome (Xi) is inherently susceptible to genomic aberrations. Replication stress (RS) has been proposed as an underlying cause, but the mechanisms that protect from Xi instability remain unknown. Here, we show that macroH2A1.2, an RS-protective histone variant enriched on the Xi, is required for Xi integrity and female survival. Mechanistically, macroH2A1.2 counteracts its structurally distinct and equally Xi-enriched alternative splice variant, macroH2A1.1. Comparative proteomics identified a role for macroH2A1.1 in alternative end joining (alt-EJ), which accounts for Xi anaphase defects in the absence of macroH2A1.2. Genomic instability was rescued by simultaneous depletion of macroH2A1.1 or alt-EJ factors, and mice deficient for both macroH2A1 variants harbor no overt female defects. Notably, macroH2A1 splice variant imbalance affected alt-EJ capacity also in tumor cells. Together, these findings identify macroH2A1 splicing as a modulator of genome maintenance that ensures Xi integrity and may, more broadly, predict DNA repair outcome in malignant cells.
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Affiliation(s)
- Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Eri K Hosogane
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Eric G Sun
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, Frederick, MD 21702, USA
| | - David M Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Prabhakar R Gudla
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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9
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Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell 2020; 181:236-249. [PMID: 32302568 PMCID: PMC7376497 DOI: 10.1016/j.cell.2020.03.053] [Citation(s) in RCA: 257] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
Abstract
Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.
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Affiliation(s)
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Koch Institute for Integrative Cancer Research, Department of Biology, MIT, Cambridge, MA 02139, USA.
| | - Philipp Oberdoerffer
- Division of Cancer Biology, National Cancer Institute, NIH, Rockville, MD 20850, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna Hupalowska
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer E Rood
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ethan Cerami
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert J Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Emek Demir
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, and Siteman Cancer Center, Washington University in St. Louis, Saint Louis, MO 63108, USA
| | - Edward D Esplin
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - James M Ford
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Oncology Division, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeremy Goecks
- Computational Biology Program, Oregon Health and Science University, OR 97201, USA
| | - Sharmistha Ghosh
- Division of Cancer Prevention, National Cancer Institute, NIH, Rockville, MD 20850, USA
| | - Joe W Gray
- Center for Spatial Systems Biomedicine, Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97201, USA
| | - Justin Guinney
- Sage Bionetworks, Seattle, WA 98121, USA; Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Sean E Hanlon
- Center for Strategic Scientific Initiatives, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shannon K Hughes
- Division of Cancer Biology, National Cancer Institute, NIH, Rockville, MD 20850, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Women's Cancer Program, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, and Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Bruce E Johnson
- Department of Medical Oncology and Department of Medicine, Dana-Farber Cancer Institute and Brigham and Women's Hospital, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Ken S Lau
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tracy Lively
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Rockville, MD 20850, USA
| | - Sarah A Mazzilli
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sandro Santagata
- Ludwig Center for Cancer Research and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA; Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Denis Schapiro
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ludwig Center for Cancer Research and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Peter K Sorger
- Ludwig Center for Cancer Research and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Avrum E Spira
- Department of Medicine, Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA; Johnson & Johnson, Cambridge, MA 02142, USA
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Cancer Institute, NIH, Rockville, MD 20850, USA
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, 4004 CTRB, Children's Hospital of Philadelphia, 3501 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert B West
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Elizabeth H Williams
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Present address: Foundation Medicine, Cambridge, MA 02141, USA
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10
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Srivastava S, Ghosh S, Kagan J, Mazurchuk R, Boja E, Chuaqui R, Chavarria-Johnson E, Davidsen T, Eary J, Haim T, Hanlon S, Hewitt S, Hughes S, Jacobs P, Li J, Lively T, Lockett S, Misteli T, Nelson S, Odeh H, Ossandon M, Rosenfield S, Samimi G, Shern J, Star R, Takebe N, Tavares N, Tricoli J, Trimble T, Umar A, Velazquez J, Wang C, Zenklusen JC, Oberdoerffer P, Lee J, Kenney N. The Making of a PreCancer Atlas: Promises, Challenges, and Opportunities. Trends Cancer 2019. [DOI: 10.1016/j.trecan.2019.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Kim J, Sun C, Tran AD, Chin PJ, Ruiz PD, Wang K, Gibbons RJ, Gamble MJ, Liu Y, Oberdoerffer P. The macroH2A1.2 histone variant links ATRX loss to alternative telomere lengthening. Nat Struct Mol Biol 2019; 26:213-219. [PMID: 30833786 PMCID: PMC6537592 DOI: 10.1038/s41594-019-0192-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/23/2019] [Indexed: 01/22/2023]
Abstract
The growth of telomerase-deficient cancers depends on the alternative lengthening of telomeres (ALT), a homology-directed telomere-maintenance pathway. ALT telomeres exhibit a unique chromatin environment and generally lack the nucleosome remodeler ATRX, pointing to an epigenetic basis for ALT. Recently, we identified a protective role for the ATRX-interacting macroH2A1.2 histone variant during homologous recombination and replication stress (RS). Consistent with an inherent susceptibility to RS, we show that human ALT telomeres are highly enriched for macroH2A1.2. However, in contrast to ATRX-proficient cells, ALT telomeres transiently lose macroH2A1.2 during acute RS to facilitate DNA double-strand break (DSB) formation, a process that is almost completely prevented by ectopic ATRX expression. Telomeric macroH2A1.2 is re-deposited in a DNA damage response (DDR)-dependent manner to promote homologous recombination-associated ALT pathways. Our findings thus identify the dynamic exchange of macroH2A1.2 on chromatin as an epigenetic link among ATRX loss, RS-induced DDR initiation and telomere maintenance via homologous recombination.
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Affiliation(s)
- Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chongkui Sun
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Pei-Ju Chin
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
- Tissue Microbiology Laboratory, Food and Drug Administration, Silver Spring, MD, USA
| | - Penelope D Ruiz
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY, USA
| | - Kun Wang
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Richard J Gibbons
- Medical Research Council, Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliff Hospital, Oxford, UK
| | - Matthew J Gamble
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yie Liu
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD, USA.
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA.
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12
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Kim J, Oberdoerffer P, Khurana S. The histone variant macroH2A1 is a splicing-modulated caretaker of genome integrity and tumor growth. Mol Cell Oncol 2018; 5:e1441629. [PMID: 30250894 DOI: 10.1080/23723556.2018.1441629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 01/14/2018] [Indexed: 02/02/2023]
Abstract
The macroH2A1.2 histone variant facilitates the response to replication stress with implications for genome maintenance and cell growth. A mutually exclusive splice variant, macroH2A1.1, has opposing effects on DNA repair outcome and proliferation. Here we discuss the potential impact of splicing-modulated macroH2A1 chromatin organization for cell function and malignant transformation.
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Affiliation(s)
- Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Simran Khurana
- National Institute for Allergy and infectious Diseases, NIH, Bethesda, MD, USA
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13
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Kim J, Sturgill D, Sebastian R, Khurana S, Tran AD, Edwards GB, Kruswick A, Burkett S, Hosogane EK, Hannon WW, Weyemi U, Bonner WM, Luger K, Oberdoerffer P. Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions. Mol Cell 2017; 69:36-47.e7. [PMID: 29249653 DOI: 10.1016/j.molcel.2017.11.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/05/2017] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
Abstract
Recent integrative epigenome analyses highlight the importance of functionally distinct chromatin states for accurate cell function. How these states are established and maintained is a matter of intense investigation. Here, we present evidence for DNA damage as an unexpected means to shape a protective chromatin environment at regions of recurrent replication stress (RS). Upon aberrant fork stalling, DNA damage signaling and concomitant H2AX phosphorylation coordinate the FACT-dependent deposition of macroH2A1.2, a histone variant that promotes DNA repair by homologous recombination (HR). MacroH2A1.2, in turn, facilitates the accumulation of the tumor suppressor and HR effector BRCA1 at replication forks to protect from RS-induced DNA damage. Consequently, replicating primary cells steadily accrue macroH2A1.2 at fragile regions, whereas macroH2A1.2 loss in these cells triggers DNA damage signaling-dependent senescence, a hallmark of RS. Altogether, our findings demonstrate that recurrent DNA damage contributes to the chromatin landscape to ensure the epigenomic integrity of dividing cells.
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Affiliation(s)
- Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Simran Khurana
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Garrett B Edwards
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Alex Kruswick
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Eri K Hosogane
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - William W Hannon
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Urbain Weyemi
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William M Bonner
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Abstract
Accurate maintenance of genomic as well as epigenomic integrity is critical for proper cell and organ function. Continuous exposure to DNA damage is, thus, often associated with malignant transformation and degenerative diseases. A significant, chronic threat to genome integrity lies in the process of transcription, which can result in the formation of potentially harmful RNA : DNA hybrid structures (R-loops) and has been linked to DNA damage accumulation as well as dynamic chromatin reorganization. In sharp contrast, recent evidence suggests that active transcription, the resulting transcripts as well as R-loop formation can play multi-faceted roles in maintaining and restoring genome integrity. Here, we will discuss the emerging contributions of transcription as both a source of DNA damage and a mediator of DNA repair. We propose that both aspects have significant implications for genome maintenance, and will speculate on possible long-term consequences for the epigenetic integrity of transcribing cells.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Robin Sebastian
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, Room B907, Bethesda, MD 20892, USA
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15
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Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, Misteli T. Abstract PR03: A lncRNA regulates DNA repair by homologous recombination. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-pr03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Long non-coding RNAs (lncRNAs) have been shown to contribute to DNA damage response (DDR) by regulating gene expression. However, very little is known about the role that lncRNAs play in regulating DNA repair. In this study we characterized a lncRNA that regulates DNA repair by Homologous recombination (HR) by modulating recruitment of DNA repair factors at the sites of DNA damage.
Experimental procedures: Control or DNA damage treated cells were processed for gene expression analysis, qPCR, live cell imaging, Immunochemistry, Western blotting, FISH and RNA Immunoprecipitation.
Results: Using a genome-wide microarray screen we identified a novel ubiquitously expressed lncRNA, DDSR1 (DNA damage-sensitive RNA 1), which is induced upon DNA damage by several DNA double-strand break (DSB) agents. DDSR1 induction upon DNA damage is dependent on the ATM-NF-kB pathway. Loss of DDSR1 impairs cell proliferation, DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect upon DDSR1 knockdown is characterized by aberrant BRCA1 and RAP80 accumulation at DSB sites. DDSR1 interacts with hnRNPUL1, an RNA-binding protein involved in HR. Loss of hnRNPUL1 also results in aberrant BRCA1 and RAP80 recruitment at DSB sites. Our results indicate that DDSR1/hnRNPUL1 depletion results in HR inhibition due to reduced end resection caused by aberrant BRCA1 and RAP80 at DSBs.
Conclusions: Our results reveal a previously unknown lncRNA involved in regulation of DDR by contributing DNA repair by HR. Our findings highlight the importance of DDSR1 in maintaining genome stability.
Citation Format: Vivek Sharma, Simran Khurana, Nard Kubben, Kotb Abdelmohsen, Philipp Oberdoerffer, Myriam Gorospe, Tom Misteli. A lncRNA regulates DNA repair by homologous recombination. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr PR03.
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Kim J, Sturgill D, Tran AD, Sinclair DA, Oberdoerffer P. Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability. Nucleic Acids Res 2015; 44:e64. [PMID: 26687720 PMCID: PMC4838352 DOI: 10.1093/nar/gkv1482] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/07/2015] [Indexed: 02/06/2023] Open
Abstract
DNA double-strand breaks (DSBs) and their repair can cause extensive epigenetic changes. As a result, DSBs have been proposed to promote transcriptional and, ultimately, physiological dysfunction via both cell-intrinsic and cell-non-autonomous pathways. Studying the consequences of DSBs in higher organisms has, however, been hindered by a scarcity of tools for controlled DSB induction. Here, we describe a mouse model that allows for both tissue-specific and temporally controlled DSB formation at ∼140 defined genomic loci. Using this model, we show that DSBs promote a DNA damage signaling-dependent decrease in gene expression in primary cells specifically at break-bearing genes, which is reversed upon DSB repair. Importantly, we demonstrate that restoration of gene expression can occur independently of cell cycle progression, underlining its relevance for normal tissue maintenance. Consistent with this, we observe no evidence for persistent transcriptional repression in response to a multi-day course of continuous DSB formation and repair in mouse lymphocytes in vivo Together, our findings reveal an unexpected capacity of primary cells to maintain transcriptome integrity in response to DSBs, pointing to a limited role for DNA damage as a mediator of cell-autonomous epigenetic dysfunction.
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Affiliation(s)
- Jeongkyu Kim
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
| | - David A Sinclair
- The Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Philipp Oberdoerffer
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, 41 Library Drive, Bethesda, MD 20892, USA
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Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, Misteli T. A BRCA1-interacting lncRNA regulates homologous recombination. EMBO Rep 2015; 16:1520-34. [PMID: 26412854 DOI: 10.15252/embr.201540437] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/25/2015] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are important players in diverse biological processes. Upon DNA damage, cells activate a complex signaling cascade referred to as the DNA damage response (DDR). Using a microarray screen, we identify here a novel lncRNA, DDSR1 (DNA damage-sensitive RNA1), which is induced upon DNA damage. DDSR1 induction is triggered in an ATM-NF-κB pathway-dependent manner by several DNA double-strand break (DSB) agents. Loss of DDSR1 impairs cell proliferation and DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect in the absence of DDSR1 is marked by aberrant accumulation of BRCA1 and RAP80 at DSB sites. In line with a role in regulating HR, DDSR1 interacts with BRCA1 and hnRNPUL1, an RNA-binding protein involved in DNA end resection. Our results suggest a role for the lncRNA DDSR1 in modulating DNA repair by HR.
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Affiliation(s)
- Vivek Sharma
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Nard Kubben
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
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18
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Oberdoerffer P. Stop relaxing: How DNA damage-induced chromatin compaction may affect epigenetic integrity and disease. Mol Cell Oncol 2014; 2:e970952. [PMID: 27308388 PMCID: PMC4905243 DOI: 10.4161/23723548.2014.970952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 09/12/2014] [Accepted: 09/13/2014] [Indexed: 11/25/2022]
Abstract
DNA damage is widely recognized for its potential to impair epigenetic integrity. Epigenetic defects are closely associated with a variety of diseases. We have recently uncovered DNA double-strand break-induced chromatin condensation as a critical modulator of repair outcome. Here, we discuss the possible implications for cell functions beyond repair.
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Affiliation(s)
- Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression. National Cancer Institute; NIH ; Bethesda, MD USA
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19
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Khurana S, Kruhlak MJ, Kim J, Tran AD, Liu J, Nyswaner K, Shi L, Jailwala P, Sung MH, Hakim O, Oberdoerffer P. A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance. Cell Rep 2014; 8:1049-62. [PMID: 25131201 PMCID: PMC4154351 DOI: 10.1016/j.celrep.2014.07.024] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 04/28/2014] [Accepted: 07/16/2014] [Indexed: 02/07/2023] Open
Abstract
Appropriate DNA double-strand break (DSB) repair factor choice is essential for ensuring accurate repair outcome and genomic integrity. The factors that regulate this process remain poorly understood. Here, we identify two repressive chromatin components, the macrohistone variant macroH2A1 and the H3K9 methyltransferase and tumor suppressor PRDM2, which together direct the choice between the antagonistic DSB repair mediators BRCA1 and 53BP1. The macroH2A1/PRDM2 module mediates an unexpected shift from accessible to condensed chromatin that requires the ataxia telangiectasia mutated (ATM)-dependent accumulation of both proteins at DSBs in order to promote DSB-flanking H3K9 dimethylation. Remarkably, loss of macroH2A1 or PRDM2, as well as experimentally induced chromatin decondensation, impairs the retention of BRCA1, but not 53BP1, at DSBs. As a result, mac-roH2A1 and/or PRDM2 depletion causes epistatic defects in DSB end resection, homology-directed repair, and the resistance to poly(ADP-ribose) polymerase (PARP) inhibition—all hallmarks of BRCA1-deficient tumors. Together, these findings identify dynamic, DSB-associated chromatin reorganization as a critical modulator of BRCA1-dependent genome maintenance.
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Affiliation(s)
- Simran Khurana
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | - Jinping Liu
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Lei Shi
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Parthav Jailwala
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA.
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20
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Liu J, Kim J, Oberdoerffer P. Metabolic modulation of chromatin: implications for DNA repair and genomic integrity. Front Genet 2013; 4:182. [PMID: 24065984 PMCID: PMC3779809 DOI: 10.3389/fgene.2013.00182] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/27/2013] [Indexed: 01/06/2023] Open
Abstract
The maintenance of genomic integrity in response to DNA damage is tightly linked to controlled changes in the damage-proximal chromatin environment. Many of the chromatin modifying enzymes involved in DNA repair depend on metabolic intermediates as cofactors, suggesting that changes in cellular metabolism can have direct consequences for repair efficiency and ultimately, genome stability. Here, we discuss how metabolites may contribute to DNA double-strand break repair, and how alterations in cellular metabolism associated with both aging and tumorigenesis may affect the integrity of our genomes.
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Affiliation(s)
- Jinping Liu
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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21
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Singh SK, Williams CA, Klarmann K, Burkett SS, Keller JR, Oberdoerffer P. Sirt1 ablation promotes stress-induced loss of epigenetic and genomic hematopoietic stem and progenitor cell maintenance. J Biophys Biochem Cytol 2013. [DOI: 10.1083/jcb2014oia6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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22
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Singh SK, Williams CA, Klarmann K, Burkett SS, Keller JR, Oberdoerffer P. Sirt1 ablation promotes stress-induced loss of epigenetic and genomic hematopoietic stem and progenitor cell maintenance. ACTA ACUST UNITED AC 2013; 210:987-1001. [PMID: 23630229 PMCID: PMC3646499 DOI: 10.1084/jem.20121608] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Loss of Sirt1 causes increased Hoxa9 expression and expansion of HSPC subsets under hematopoietic stress, resulting in increased DNA damage and exhaustion of long-term progenitors. The (histone) deacetylase Sirt1 is a mediator of genomic and epigenetic maintenance, both of which are critical aspects of stem cell homeostasis and tightly linked to their functional decline in aging and disease. We show that Sirt1 ablation in adult hematopoietic stem and progenitor cells (HSPCs) promotes aberrant HSPC expansion specifically under conditions of hematopoietic stress, which is associated with genomic instability as well as the accumulation of DNA damage and eventually results in a loss of long-term progenitors. We further demonstrate that progenitor cell expansion is mechanistically linked to the selective up-regulation of the HSPC maintenance factor and polycomb target gene Hoxa9. We show that Sirt1 binds to the Hoxa9 gene, counteracts acetylation of its histone target H4 lysine 16, and in turn promotes polycomb-specific repressive histone modification. Together, these findings demonstrate a dual role for Sirt1 in HSPC homeostasis, both via epigenetic regulation of a key developmental gene and by promoting genome stability in adult stem cells.
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Affiliation(s)
- Satyendra K Singh
- Mouse Cancer Genetics Program, SAIC-Frederick, Inc, Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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23
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Burgess RC, Misteli T, Oberdoerffer P. DNA damage, chromatin, and transcription: the trinity of aging. Curr Opin Cell Biol 2012; 24:724-30. [PMID: 22902297 DOI: 10.1016/j.ceb.2012.07.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 07/25/2012] [Indexed: 01/01/2023]
Abstract
Aging brings about numerous cellular defects. Amongst the most prominent are elevated levels of persistent DNA damage, changes to chromatin structure and epigenetic modifications, and alterations of global transcription programs. These are not independent events and recent work begins to shed light on the intricate interplay between these aging-related defects.
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Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2012; 479:74-9. [PMID: 21964334 DOI: 10.1038/nature10442] [Citation(s) in RCA: 718] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 11/03/2011] [Accepted: 08/12/2011] [Indexed: 12/17/2022]
Abstract
Alternative splicing of pre-messenger RNA is a key feature of transcriptome expansion in eukaryotic cells, yet its regulation is poorly understood. Spliceosome assembly occurs co-transcriptionally, raising the possibility that DNA structure may directly influence alternative splicing. Supporting such an association, recent reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns. Moreover, the rate of transcription elongation has been linked to alternative splicing. Here we provide the first evidence that a DNA-binding protein, CCCTC-binding factor (CTCF), can promote inclusion of weak upstream exons by mediating local RNA polymerase II pausing both in a mammalian model system for alternative splicing, CD45, and genome-wide. We further show that CTCF binding to CD45 exon 5 is inhibited by DNA methylation, leading to reciprocal effects on exon 5 inclusion. These findings provide a mechanistic basis for developmental regulation of splicing outcome through heritable epigenetic marks.
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Affiliation(s)
- Sanjeev Shukla
- Center for Cancer Research, Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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25
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Shi L, Oberdoerffer P. Chromatin dynamics in DNA double-strand break repair. Biochim Biophys Acta 2012; 1819:811-9. [PMID: 22285574 DOI: 10.1016/j.bbagrm.2012.01.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/28/2011] [Accepted: 01/05/2012] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks (DSBs) occur in the context of a highly organized chromatin environment and are, thus, a significant threat to the epigenomic integrity of eukaryotic cells. Changes in break-proximal chromatin structure are thought to be a prerequisite for efficient DNA repair and may help protect the structural integrity of the nucleus. Unlike most bona fide DNA repair factors, chromatin influences the repair process at several levels: the existing chromatin context at the site of damage directly affects the access and kinetics of the repair machinery; DSB induced chromatin modifications influence the choice of repair factors, thereby modulating repair outcome; lastly, DNA damage can have a significant impact on chromatin beyond the site of damage. We will discuss recent findings that highlight both the complexity and importance of dynamic and tightly orchestrated chromatin reorganization to ensure efficient DSB repair and nuclear integrity. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Lei Shi
- Mouse Cancer Genetics Program, NCI- Frederick, NIH, Frederick, MD 21702, USA
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26
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Baur JA, Chen D, Chini EN, Chua K, Cohen HY, de Cabo R, Deng C, Dimmeler S, Gius D, Guarente LP, Helfand SL, Imai SI, Itoh H, Kadowaki T, Koya D, Leeuwenburgh C, McBurney M, Nabeshima YI, Neri C, Oberdoerffer P, Pestell RG, Rogina B, Sadoshima J, Sartorelli V, Serrano M, Sinclair DA, Steegborn C, Tatar M, Tissenbaum HA, Tong Q, Tsubota K, Vaquero A, Verdin E. Dietary restriction: standing up for sirtuins. Science 2010; 329:1012-3; author reply 1013-4. [PMID: 20798296 DOI: 10.1126/science.329.5995.1012] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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27
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Sinclair DA, Oberdoerffer P. The ageing epigenome: damaged beyond repair? Ageing Res Rev 2009; 8:189-98. [PMID: 19439199 DOI: 10.1016/j.arr.2009.04.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 04/30/2009] [Accepted: 04/30/2009] [Indexed: 12/28/2022]
Abstract
Of all the proposed causes of ageing, DNA damage remains a leading, though still debated theory. Unlike most other types of age-related cellular damage, which can hypothetically be reversed, mutations in DNA are permanent. Such errors result in the accumulation of changes to RNA and protein sequences with age, and are tightly linked to cellular senescence and overall organ dysfunction. Over the past few years, an additional, more global role has emerged for the contribution of DNA damage and genomic instability to the ageing process. We, and others have found that DNA damage and the concomitant repair process can induce genome-wide epigenetic changes, which may promote a variety of age-related transcriptional and functional changes. Here, we discuss the link between DNA damage, chromatin alterations and ageing, an interplay that explains how seemingly random DNA damage could manifest in predictable phenotypic changes that define ageing, changes that may ultimately be reversible.
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28
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Firestein R, Blander G, Michan S, Oberdoerffer P, Ogino S, Campbell J, Bhimavarapu A, Luikenhuis S, de Cabo R, Fuchs C, Hahn WC, Guarente LP, Sinclair DA. The SIRT1 deacetylase suppresses intestinal tumorigenesis and colon cancer growth. PLoS One 2008; 3:e2020. [PMID: 18414679 PMCID: PMC2289879 DOI: 10.1371/journal.pone.0002020] [Citation(s) in RCA: 473] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 03/11/2008] [Indexed: 02/07/2023] Open
Abstract
Numerous longevity genes have been discovered in model organisms and altering their function results in prolonged lifespan. In mammals, some have speculated that any health benefits derived from manipulating these same pathways might be offset by increased cancer risk on account of their propensity to boost cell survival. The Sir2/SIRT1 family of NAD(+)-dependent deacetylases is proposed to underlie the health benefits of calorie restriction (CR), a diet that broadly suppresses cancer in mammals. Here we show that CR induces a two-fold increase SIRT1 expression in the intestine of rodents and that ectopic induction of SIRT1 in a beta-catenin-driven mouse model of colon cancer significantly reduces tumor formation, proliferation, and animal morbidity in the absence of CR. We show that SIRT1 deacetylates beta-catenin and suppresses its ability to activate transcription and drive cell proliferation. Moreover, SIRT1 promotes cytoplasmic localization of the otherwise nuclear-localized oncogenic form of beta-catenin. Consistent with this, a significant inverse correlation was found between the presence of nuclear SIRT1 and the oncogenic form of beta-catenin in 81 human colon tumor specimens analyzed. Taken together, these observations show that SIRT1 suppresses intestinal tumor formation in vivo and raise the prospect that therapies targeting SIRT1 may be of clinical use in beta-catenin-driven malignancies.
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Affiliation(s)
- Ron Firestein
- Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana Farber Cancer Institute, and Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
| | - Gil Blander
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shaday Michan
- Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Philipp Oberdoerffer
- Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Jennifer Campbell
- Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Anupama Bhimavarapu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sandra Luikenhuis
- Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rafael de Cabo
- Laboratory of Experimental Gerontology, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Charles Fuchs
- Department of Medical Oncology, Dana Farber Cancer Institute, and Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
| | - William C. Hahn
- Department of Medical Oncology, Dana Farber Cancer Institute, and Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
| | - Leonard P. Guarente
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - David A. Sinclair
- Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Department of Pathology, Harvard Medical School, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Abstract
Eukaryotes come in many shapes and sizes, yet one thing that they all seem to share is a decline in vitality and health over time--a process known as ageing. If there are conserved causes of ageing, they may be traced back to common biological structures that are inherently difficult to maintain throughout life. One such structure is chromatin, the DNA-protein complex that stabilizes the genome and dictates gene expression. Studies in the budding yeast Saccharomyces cerevisiae have pointed to chromatin reorganization as a main contributor to ageing in that species, which raises the possibility that similar processes underlie ageing in more complex organisms.
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Affiliation(s)
- Philipp Oberdoerffer
- Department of Pathology, Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts, USA
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30
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Oberdoerffer P, Kanellopoulou C, Heissmeyer V, Paeper C, Borowski C, Aifantis I, Rao A, Rajewsky K. Efficiency of RNA interference in the mouse hematopoietic system varies between cell types and developmental stages. Mol Cell Biol 2005; 25:3896-905. [PMID: 15870264 PMCID: PMC1087705 DOI: 10.1128/mcb.25.10.3896-3905.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RNA interference (RNAi) is a naturally occurring posttranscriptional gene-silencing mechanism that has been adapted as a genetic tool for loss-of-function studies of a variety of organisms. It is more widely applicable than classical gene targeting and allows for the simultaneous inactivation of several homologous genes with a single transgene. Recently, RNAi has been used for conditional and conventional gene inactivation in mice. Unlike gene targeting, RNAi is a dynamic process, and its efficiency may vary both between cell types and throughout development. Here we demonstrate that RNAi can be used to target three separately encoded isoforms of the bcl-2 family gene bfl-1/A1 in a conditional manner in mice. The extent of gene inactivation varies between different cell types and is least efficient in mature lymphocytes. Our data suggest that RNAi is affected by factors beyond small interfering RNA-mRNA stoichiometry.
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Affiliation(s)
- Philipp Oberdoerffer
- The CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA.
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31
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Mandal M, Borowski C, Palomero T, Ferrando AA, Oberdoerffer P, Meng F, Ruiz-Vela A, Ciofani M, Zuniga-Pflucker JC, Screpanti I, Look AT, Korsmeyer SJ, Rajewsky K, von Boehmer H, Aifantis I. The BCL2A1 gene as a pre-T cell receptor-induced regulator of thymocyte survival. ACTA ACUST UNITED AC 2005; 201:603-14. [PMID: 15728238 PMCID: PMC2213063 DOI: 10.1084/jem.20041924] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The pre–T cell receptor (TCR) is expressed early during T cell development and imposes a tight selection for differentiating T cell progenitors. Pre-TCR–expressing cells are selected to survive and differentiate further, whereas pre-TCR− cells are “negatively” selected to die. The mechanisms of pre-TCR–mediated survival are poorly understood. Here, we describe the induction of the antiapoptotic gene BCL2A1 (A1) as a potential mechanism regulating inhibition of pre–T cell death. We characterize in detail the signaling pathway involved in A1 induction and show that A1 expression can induce pre–T cell survival by inhibiting activation of caspase-3. Moreover, we show that in vitro “knockdown” of A1 expression can compromise survival even in the presence of a functional pre-TCR. Finally, we suggest that pre-TCR–induced A1 overexpression can contribute to T cell leukemia in both mice and humans.
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Affiliation(s)
- Malay Mandal
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
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32
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Oberdoerffer P, Otipoby KL, Maruyama M, Rajewsky K. Unidirectional Cre-mediated genetic inversion in mice using the mutant loxP pair lox66/lox71. Nucleic Acids Res 2004; 31:e140. [PMID: 14602933 PMCID: PMC275577 DOI: 10.1093/nar/gng140] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The Cre/loxP recombination system is a commonly used tool to alter the mouse genome in a conditional manner by deletion or inversion of loxP-flanked DNA segments. While Cre-mediated deletion is essentially unidirectional, inversion is reversible and therefore does not allow the stable alteration of gene function in cells that constitutively express Cre. Site-directed mutagenesis yielded a pair of asymmetric loxP sites (lox66 and lox71) that display a favorable forward reaction equilibrium. Here, we demonstrate that lox66/lox71 mediates efficient and predominantly unidirectional inversion of a switch substrate targeted to the mouse genome in combination with either inducible or cell type-specific cre-transgenes in vivo.
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Affiliation(s)
- Philipp Oberdoerffer
- The CBR Institute for Biomedical Research, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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33
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Oberdoerffer P, Novobrantseva TI, Rajewsky K. Expression of a targeted lambda 1 light chain gene is developmentally regulated and independent of Ig kappa rearrangements. J Exp Med 2003; 197:1165-72. [PMID: 12719477 PMCID: PMC2193966 DOI: 10.1084/jem.20030402] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Immunoglobulin light chain (IgL) rearrangements occur more frequently at Ig kappa than at Ig lambda. Previous results suggested that the unrearranged Ig kappa locus negatively regulates Ig lambda transcription and/or rearrangement. Here, we demonstrate that expression of a VJ lambda 1-joint inserted into its physiological position in the Ig lambda locus is independent of Ig kappa rearrangements. Expression of the inserted VJ lambda 1 gene segment is developmentally controlled like that of a VJ kappa-joint inserted into the Ig kappa locus and furthermore coincides developmentally with the occurrence of Ig kappa rearrangements in wild-type mice. We conclude that developmentally controlled transcription of a gene rearrangement in the Ig lambda locus occurs in the presence of an unrearranged Ig kappa locus and is therefore not negatively regulated by the latter. Our data also indicate light chain editing in approximately 30% of lambda 1 expressing B cell progenitors.
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Affiliation(s)
- Philipp Oberdoerffer
- Center for Blood Research, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
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