DNA Damage and P53: Target Gene Selection and Signaling Dynamics

Total Page:16

File Type:pdf, Size:1020Kb

DNA Damage and P53: Target Gene Selection and Signaling Dynamics DNA damage and p53: target gene selection and signaling dynamics Jacob Stewart-Ornstein Dept. Computational and Systems Biology University of Pittsburgh & Hillman Cancer Center Stress is Universal Environmental Fluctuations Poisons = Infection Radiation Stress Response Molecular Pathways that respond to cellular damage and: (1) Adjust the cell to its new environment (2) Repair Any Damage Stress responses are ubiquitous and conserved Conserved from yeast, Human Nutrient (m)TOR, RAS, GCN2/4 Heat HSF1 Oxidative NRF2 Hypoxia HIF1 ER IRE1/XBP1, PERK, ATF6 DNA damage ATM/ATR, tp53 Vihervaara… Lis, Nat. Rev. Gen., 2018 Stress responses act to restore homeostasis UPR response in Budding Yeast Response 1mM DTT 2mM DTT Growth Rate Time (~hrs) Pincus et al., 2010, PLOS Bio In multicellular systems stress responses specify cell fate Response Damage Cell death Response Resumption Cell death of growth Dose of DNA damage determines cell fate damage γH2AX Dapi Cell cycle arrest Apoptosis + Repair Or Senescence How can the cell determine its DNA damage status? damage γH2AX Dapi Apoptosis Cell cycle arrest Or + Repair Senescence Appropriate # breaks Transcriptional response Tissue specificity of DNA damage signaling # breaks Cell fate Small Intestine Spleen (5Gy IR) (5Gy Tunel , DAPI Outline (1) How does the cell respond proportionately to DNA damage? (2) How universal is the transcriptional response to DNA damage? When cells are treated with radiation IR dose # Breaks (~dose2) γH2AX Viability DAPI What is the transcriptional response to IR? IR dose # Breaks (~dose2) γH2AX Transcriptional Response? Linear Saturating Response Response dose dose What signaling Pathways are activated by DNA damage? Human Cell Lines x12 RNAseq + Ionizing Radiation What pathways are enriched? Number of of Number Genes Z-Score ΔGene Expression The transcriptional response to radiation is dominated by p53 Human Cell Lines x12 p53 Number of of Number Genes p53 (e-21) Highly conserved DNA damage responsive factor Z-Score ΔGene Expression The transcriptional response to radiation is dominated by p53 Human Cell Lines Mouse Tissues x12 x5 Number of of Number Genes p53 (e-21) p53 (e-35) Z-Score ΔGene Expression Z-Score ΔGene Expression Knockdown of p53 largely eliminates the short term transcriptional response to radiation in epithelial cells Significantly induced transcripts 6 5 4 3 2 1 Number of of Number Genes 0 p53 (e-21) Log2 Fold Change p53sh 90% (43/48) -1 p53 dependent -2 1 2 3 4 5 6 Log2 Fold Change WT Z-Score ΔGene Expression p53 Determines DNA damage Sensitivity thymocytes p53-/- p53+/- p53+/+ Lowe… Jacks, 1993, nature p53 Determines DNA damage Sensitivity thymocytes 2 p53 1.5 -/- p53 1 0.5 0 -0.5 p53+/- -1 Cisplatin Treated Fitness -1.5 +/+ p53 -2 -2 -1 0 1 2 Untreated Fitness CAS9 Screen A549 Lowe… Jacks, 1993, nature p53 is the key DNA damage responsive transcription factor DNA ATM Cell Cycle Arrest Oxidative Stress Apoptosis p53 Hypoxia DNA Repair Translational Stress DeLeo et al., 1979 Crawford et al., 1979 Metabolism Finlay et al., 1989 Farmer et al., 1992 El-Deiry et al., 1993 Harper et al., 1993 … How does the cell respond transcriptionally to DNA damage? IR dose # Breaks (~dose2) γH2AX p53? p53? dose dose Acute response to DNA damage is not dose sensitive +DNA damage p53 Log2 Dose p53 dose Longer Term response to DNA damage is dose dependent p53 Log2 Dose dose Across 12 human cell lines the acute p53 response is dose invariant, but the longer term response depends on DNA damage Models of p53 signaling Duration of signaling is dose sensitive Response Response Need real time reporters of p53 signaling! A live cell reporter of p53 activity reveals complex dynamics MCF7 (breast cancer) p53-YFP In response to DNA damage a negative feedback loop drives oscillations of p53 DNA ATM p53 p53-YFP MDM2 In response to DNA damage a negative feedback loop drives oscillations of p53 60 p53 50 DNA YFP(AU) - 40 30 P53 0 5 10 15 20 25 30 35 250 MDM2 ATM 200 150 100 p53 0 5 10 15 20 25 30 35 p53-YFP MDM2 In response to DNA damage a negative feedback loop drives oscillations of p53 60 p53 50 DNA YFP(AU) - 40 30 P53 0 5 10 15 20 25 30 35 250 MDM2 ATM 200 150 100 p53 0 5 10 15 20 25 30 35 P53->MDM2 P53 period ~5hr MDM2 1 0.6 0.4 0.5 0.2 0 0 Autocorrelation Crosscorrelation -0.5 -0.2 0 2 4 6 8 0 1 2 3 4 Time (hrs) Time (hrs) Recapitulates results from Lahav, 2004 Given oscillations, how is dose encoded? DNA DNA ATM ATM p53 vs p53 MDM2 MDM2 In MCF7 number of ‘pulses’ of p53 is controlled by dose Signaling is duration encoded 4 3.5 Low IR (1Gy) 3 2.5 2 1.5 P53 (AU) 1 0.5 0 -0.5 0 5 10 15 20 25 Dose proportional # Pulses 4 Dose is not proportional to Amplitude 3.5 High IR (8Gy) 3 2.5 2 1.5 1 P53 (AU) 0.5 0 -0.5 0 5 10 15 20 25 Time after IR (hrs) Analysis of p53 dynamics across 12 cell lines Dose (Gy) Low IR (1Gy) High IR (8Gy) YFP (AU) - p53 Time Time Other cell lines show both duration and amplitude control Dose (Gy) Low IR (1Gy) High IR (8Gy) YFP (AU) - p53 Time Time In A549s amplitude of p53 is regulated by dose 6 Low IR (1Gy) Low IR (1Gy) 5 4 3 P53 (AU) 2 1 0 0 5 10 15 20 25 10 High IR (8Gy) 8 High IR (8Gy) 6 4 P53 (AU) 2 0 0 5 10 15 20 25 Time after IR (hrs) Why do some cell lines show amplitude vs duration response to DNA damage dose? Low IR (1Gy) High IR (8Gy) Duration MCF7 Time A549 Amplitude Chemical Screen for p53 dose response behavior High IR (8Gy) Kinase inhibitor screen for dynamics P53 (AU) Drug screen P53 (AU) Time In maximum A549 amplitude of p53 is regulated by dose High IR (8Gy) P53 (AU) Drug screen P53 (AU) Time Cell types with low ATM levels show reduced dynamic range In p53 signaling DNA MCF7 ATM act ATM p53 ATM pATM DNA damage (AU) p53 A549 ATM act ATM p53 MDM2 DNA damage (AU) Cell types with low ATM levels show reduced dynamic range In p53 signaling 8Gy IR A549 Time UO31 UACC62 6 5 4 MCF7 3 HCT116 2 frequency 1 0 -4 -3 -2 -1 0 1 2 Log ATMact (AU) A general model reconciling p53 response and ATM activity DNA DNA* ATM p53 MDM2 Stewart-Ornstein and Lahav., Science Signaling, 2017 Stewart-Ornstein and Lahav., Current Opinion is Systems Biology, 2017 Outline (1) How does the cell respond proportionately to DNA damage? -duration or amplitude of p53 signaling are proportional to DNA damage -balance between amplitude and duration signaling is cell lines specific -ATM is a regulator of the dynamic range of p53 (2) Do all cells respond to DNA damage in the same way? Is the p53 transcriptional response uniform? A diverse set of cell lines to model variation in DNA damage response 12 Human Cell Lines x12 All express WT p53 Range of Radiosensitivites EC50: 1-3Gy Before and After DNA damage p53 levels are comparable Across 12 cell lines Fold change after damage 1.5-3.5 2 1.5 1 0.5 p53 Fold Change p53 Fold Change log2 p53 Change Fold 0 What is p53 doing in each cell line? What is p53 binding to? ChIP-seq to measure p53 binding in the genome p53 binding in the genome is quite stereotyped 2hrs after IR treatment (4Gy) Different cell lines show quantitatively similar binding Pearson R in dataset ranged from 0.5-0.75 p53 binding is stereotyped, with some exceptions Some universal, some cell type specific p53 targets IL1A GREB1 ~5% of p53 binding sites show variability across cell lines IL1A GREB1 Why would p53 bind different locations in different cell lines? Cofactors or Chromatin Access? Variation in p53 binding can be explained by chromatin accessibility (measured with Mu-Transposase ATACseq) MCF7 LOXIMVI variation in p53 binding can be explained by chromatin accessibility MCF7 LOXIMVI GREB1 IL1A variation in p53 binding can be explained by chromatin accessibility More accessible in LOXIMVI Differential atac seq signaling explains 22% of the variance in p53 binding More accessible in MCF7 Does chromatin regulate p53 binding or does p53 regulate chromatin? Regulated by Chromatin “pioneer factor” No. For core targets of p53 chromatin does not need to be open p21 PUMA MDM2 Consistent with Genome Res. 2015 Sammons... Berger. Treatment with DNA methylase inhibitor to test effect of increased chromatin accessibility Decitabine Treatment with DNA methylase inhibitor alters chromatin state in MCF7 cells and opens up new p53 binding sites Decitabine p53 is both a pioneer and a follower Tight Regulation by Pioneering activity at chromatin ‘poised’ sites Cell type specific ‘Universal’ Binding sites DNA binding sites Are there physiological cell states that alter p53 binding? Mesenchymal and Estrogen+ Cell States are associated with novel p53 binding IL1A GREB1 EMT A549 cells when treated with TGFB undergo EMT Does p53 binding change? +TGFB Axl dapi A549 cells forced to undergo EMT show p53 binding at the IL1 locus +TGFB Axl dapi rep1 ChIPseq p53 +TGFB rep2 +TGFB IL1 expression in +TGFB EMTed dapi Axl A549 cells depends on p53 p53 ChIPseq Log2 siTP53/siCTR p53 IL1A IL1B What happens to p53 binding when a cell becomes cancerous? 57% of cancers have WT p53 Conclusions Dose of DNA damage alters the duration and amplitude of p53 signaling -balance is controlled by ATM levels Chromatin tunes p53 binding imparting cell type specificity to the DNA damage response -- Some binding sites are ‘poised’ for p53 binding -- Other binding sites require exogenous stimuli How to think about p53? Master regulator Linear Transducer / Signal integrator Damage Cell Fate 1 Cell Fate 2 Modified from Bieging and Attardi - Trends in Cell Bio, 2015.
Recommended publications
  • EMBO Facts & Figures
    excellence in life sciences Reykjavik Helsinki Oslo Stockholm Tallinn EMBO facts & figures & EMBO facts Copenhagen Dublin Amsterdam Berlin Warsaw London Brussels Prague Luxembourg Paris Vienna Bratislava Budapest Bern Ljubljana Zagreb Rome Madrid Ankara Lisbon Athens Jerusalem EMBO facts & figures HIGHLIGHTS CONTACT EMBO & EMBC EMBO Long-Term Fellowships Five Advanced Fellows are selected (page ). Long-Term and Short-Term Fellowships are awarded. The Fellows’ EMBO Young Investigators Meeting is held in Heidelberg in June . EMBO Installation Grants New EMBO Members & EMBO elects new members (page ), selects Young EMBO Women in Science Young Investigators Investigators (page ) and eight Installation Grantees Gerlind Wallon EMBO Scientific Publications (page ). Programme Manager Bernd Pulverer S Maria Leptin Deputy Director Head A EMBO Science Policy Issues report on quotas in academia to assure gender balance. R EMBO Director + + A Conducts workshops on emerging biotechnologies and on H T cognitive genomics. Gives invited talks at US National Academy E IC of Sciences, International Summit on Human Genome Editing, I H 5 D MAN 201 O N Washington, DC.; World Congress on Research Integrity, Rio de A M Janeiro; International Scienti c Advisory Board for the Centre for Eilish Craddock IT 2 015 Mammalian Synthetic Biology, Edinburgh. Personal Assistant to EMBO Fellowships EMBO Scientific Publications EMBO Gold Medal Sarah Teichmann and Ido Amit receive the EMBO Gold the EMBO Director David del Álamo Thomas Lemberger Medal (page ). + Programme Manager Deputy Head EMBO Global Activities India and Singapore sign agreements to become EMBC Associate + + Member States. EMBO Courses & Workshops More than , participants from countries attend 6th scienti c events (page ); participants attend EMBO Laboratory Management Courses (page ); rst online course EMBO Courses & Workshops recorded in collaboration with iBiology.
    [Show full text]
  • PDCD5 Interacts with P53 and Functions As a Regulator of P53 Dynamics in the DNA Damage Response
    i \Zhuge-BJ" | 2018/6/13 | 5:45 | page 1 | #1 i i i Biophysical Journal Volume: 00 Month Year 1{12 1 PDCD5 interacts with p53 and functions as a regulator of p53 dynamics in the DNA damage response Changjing Zhugea, Xiaojuan Sunb, Yingyu Chenc, Jinzhi Leid a College of Sciences, Beijing Forestry University, 35 Tsinghua East Road, Beijing 100083, China; b School of Science, Beijing University of Posts and Telecommunications, 10 Xitucheng Road, Beijing 100876, China; c Laboratory of Medical Immunology, School of Basic Medical Science, Peking University, 38 Xueyuan Road, Beijing 100083, China; d MOE Key Laboratory of Bioinformatics, Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China Abstract The tumor suppressor p53 plays a central role in cell fate decisions after DNA damage. Programmed Cell Death 5 (PDCD5) is known to interact with the p53 pathway to promote cell apoptosis. Recombinant human PDCD5 can significantly sensitize different cancers to chemotherapies. In the present paper, we construct a computational model that includes PDCD5 interactions in the p53 signaling network and study the effects of PDCD5 on p53- mediated cell fate decisions during the DNA damage response. Our results revealed that PDCD5 functions as a co-activator of p53 that regulates p53-dependent cell fate decisions via the mediation of p53 dynamics. The effects of PDCD5 are dose-dependent such that p53 can display either sustained or pulsed dynamics at different PDCD5 levels. Moreover, PDCD5 regulates caspase-3 activation via two mechanisms during the two phases of sustained and pulsed p53 dynamics. This study provides insights regarding how PDCD5 functions as a regulator of the p53 pathway and might be helpful for increasing our understanding of the molecular mechanisms by which PDCD5 can be used to treat cancers.
    [Show full text]
  • The Pseudo-Caspase FLIP(L) Regulates Cell Fate Following P53 Activation
    The pseudo-caspase FLIP(L) regulates cell fate following p53 activation Andrea Leesa,1, Alexander J. McIntyrea,1, Nyree T. Crawforda, Fiammetta Falconea, Christopher McCanna, Caitriona Holohana, Gerard P. Quinna, Jamie Z. Robertsa, Tamas Sesslera, Peter F. Gallaghera, Gemma M. A. Gregga, Katherine McAllistera, Kirsty M. McLaughlina, Wendy L. Allena, Laurence J. Eganb, Aideen E. Ryanb,c, Melissa J. Labonte-Wilsona, Philip D. Dunnea, Mark Wappetta, Vicky M. Coylea, Patrick G. Johnstona, Emma M. Kerra, Daniel B. Longleya,2,3, and Simon S. McDadea,2,3 aPatrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom; bDiscipline of Pharmacology & Therapeutics, Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland; and cRegenerative Medicine Institute, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland Edited by Karen H. Vousden, Francis Crick Institute, London, United Kingdom, and approved June 8, 2020 (received for review February 12, 2020) p53 is the most frequently mutated, well-studied tumor-suppressor switch from cell-cycle arrest to cell death induction remain gene, yet the molecular basis of the switch from p53-induced cell- poorly understood, although p53-mediated transcriptional up- cycle arrest to apoptosis remains poorly understood. Using a combi- regulation of PUMA has been suggested to be crucial in a nation of transcriptomics and functional genomics, we unexpectedly number of studies (10, 11). identified a nodal role for the caspase-8 paralog and only human Despite p53/TP53 being the most frequently mutated gene in pseudo-caspase, FLIP(L), in regulating this switch.
    [Show full text]
  • The Puzzling Interplay Between P53 and Sp1 - Full Text
    7/20/2021 Aging | The puzzling interplay between p53 and Sp1 - Full Text Editorial Volume 9, Issue 5 pp 1355—1356 The puzzling interplay between p53 and Sp1 Ariella Oppenheim1 , Galit Lahav2 1 Department of Hematology, Hebrew University Faculty of Medicine, Jerusalem 91120, Israel 2 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA Received: May 4, 2017 Published: May 9, 2017 https://doi.org/10.18632/aging.101238 How to Cite Copyright: Oppenheim and Lahav. This is an open‐access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited The paradigm tumor suppressor protein p53 was initially discovered in the Seventies by a number of investigators as a protein that was tightly bound to SV40 large T-antigen, a “contaminant” during T-antigen purification [1]. Its role as a tumor suppressor was realized only a few years later, when it was found that it is absent or mutated in many tumors. Since then p53 has been described as the “guardian of the genome”, due to its central role in keeping genome integrity in response to genotoxic stress as well as many other insults [2]. Specificity Factor 1, Sp1, was the first mammalian transcription factor to be purified and characterized by Dynan and Tjian in the early Eighties. Sp1 is overexpressed in many types of cancer, including those carrying wild-type p53. Sp1 therefore is considered as a ‘hallmark of cancer’ and a candidate target for cancer therapy [3].
    [Show full text]
  • The Ups and Downs of P53: Proc
    PERSPECTIVES 155. Akira, S. & Takeda, K. Toll-like receptor signalling. Nature Rev. Immunol. 4, 499–511 (2004). OPINION 156. Tsenova, L., Bergtold, A., Freedman, V. H., Young, R. A. & Kaplan, G. Tumour necrosis factor α is a determinant of pathogenesis and disease progression in mycobacterial infection in the central nervous system. The ups and downs of p53: Proc. Natl Acad. Sci. USA 96, 5657–5662 (1999). 157. Schluter, D. et al. Both lymphotoxin-α and TNF are crucial for control of Toxoplasma gondii in the central nervous system. J. Immunol. 170, 6172–6182 (2003). understanding protein dynamics 158. Pasparakis, M. et al. Peyer’s patch organogenesis is intact yet formation of B lymphocyte follicles is defective in peripheral lymphoid organs of mice deficient for in single cells tumor necrosis factor and its 55-kDa receptor. Proc. Natl Acad. Sci. USA 94, 6319–6323 (1997). 159. Kuprash, D. V. et al. Novel tumor necrosis factor- Eric Batchelor, Alexander Loewer and Galit Lahav knockout mice that lack Peyer’s patches. Eur. J. Immunol. 35, 1592–1600 (2005). 160. Grivennikov, S. I. et al. Distinct and nonredundant Abstract | Cells living in a complex environment must constantly detect, process in vivo functions of TNF produced by T cells and macrophages/neutrophils: protective and deleterious and appropriately respond to changing signals. Therefore, all cellular information effects. Immunity 22, 93–104 (2005). 161. Beutler, B. et al. Identity of tumour necrosis factor and processing is dynamic in nature. As a consequence, understanding the process of the macrophage-secreted factor cachetin. Nature 316, signal transduction often requires detailed quantitative analysis of dynamic 552–554 (1985).
    [Show full text]
  • Long-Term P21 and P53 Trends Regulate the Frequency of Mitosis Events and Cell Cycle Arrest
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.17.456721; this version posted August 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Long-term p21 and p53 trends regulate the frequency of mitosis events and cell cycle arrest Anh Phong Tran1, Christopher J. Tralie2, Caroline Moosmüller3;4, Zehor Belkhatir5, José Reyes6;7, Arnold J. Levine8 Joseph O. Deasy1, Allen R. Tannenbaum9;∗ 1Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. 2Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, USA. 3Department of Mathematics, University of California, San Diego, La Jolla, CA, USA. 4Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA. 5School of Engineering and Sustainable Development, De Montfort University, Leicester, UK. 6Department of Systems Biology, Harvard Medical School, Boston, MA, USA. 7Cancer Biology and Genetics Program and Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. 8Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA. 9Departments of Computer Science and Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY, USA. ∗Corresponding author: [email protected] August 18, 2021 1 Abstract Radiation exposure of healthy cells can halt cell cycle temporarily or permanently. In this work, two single cell datasets that monitored the time evolution of p21 and p53, one subjected to gamma irradiation and the other to x-ray irradiation, are analyzed to uncover the dynamics of this process.
    [Show full text]
  • DNA-Damage-Induced Apoptosis in Stem and Cancer Cells
    DNA-damage-induced apoptosis in stem and cancer cells The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Liu, Julia Chang. 2014. DNA-damage-induced apoptosis in stem Citation and cancer cells. Doctoral dissertation, Harvard University. Accessed April 17, 2018 5:05:37 PM EDT Citable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12274582 This article was downloaded from Harvard University's DASH Terms of Use repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA (Article begins on next page) DNA-damage-induced apoptosis in stem and cancer cells A dissertation presented by Julia Chang Liu to e Committee on Higher Degrees in Biophysics in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biophysics Harvard University Cambridge, Massachusetts January © -Julia Chang Liu All rights reserved. Dissertation Advisor: Professor Galit Lahav Julia Chang Liu DNA-damage-induced apoptosis in stem and cancer cells A is work comprises analyses of cell fate decision-making in response to DNA damage. DNA damage is a ubiquitous threat to genomic stability, and depending on the type and extent of the damage, can lead to widespread changes in cell func- tion as well as cell death. How apoptosis, or programmed cell death, is triggered in damaged cells was studied in different cell types for different types of damage. Cell fate decisions are the outcome of information processing in signaling net- works.
    [Show full text]
  • ANNUAL REPORT 2019 Unding Brave and Bold
    ANNUAL REPORT 2019 unding brave and bold. Cancer. No disease in F the history of medicine has proven more elusive and resilient. It defies logic. It’s unpredictable. It hides in plain sight. It evolves. And it’s soon to be the number one killer in America. The very nature of cancer is why, at the Damon Runyon Cancer Research Foundation, OUR we believe that only by pursuing And we support them the and investing in the most best way we know how— with audacious and ambitious ideas the money they need to bring will we achieve victory over their ideas from whiteboards humankind’s deadliest enemy. to reality. The funding and freedom to pursue theories, Our research focus is singular: concepts and strategies that high-risk, high-reward. others are not brave or bold enough to bet their careers on. Research that others might deem radical or believe to be Brave and bold. reaching too far. Research that has a good chance of failure, but That’s where the Damon at the same time has a chance to Runyon Cancer Research fundamentally change the game. Foundation invests. That’s where we believe the answers Who does that kind of will come from. research? Brave and bold. Young scientists with the brilliance and unbridled passion The only two words that will to push boundaries and break beat cancer. rules. People with the incredible brainpower to earn millions of dollars on Wall Street or in Silicon Valley, but who have chosen to take a different path, a path that could instead save millions of lives.
    [Show full text]
  • DNA Damage Strength Modulates a Bimodal Switch of P53 Dynamics For
    Chen et al. BMC Biology 2013, 11:73 http://www.biomedcentral.com/1741-7007/11/73 RESEARCH ARTICLE Open Access DNA damage strength modulates a bimodal switch of p53 dynamics for cell-fate control Xi Chen1, Jia Chen2, Siting Gan2, Huaji Guan1, Yuan Zhou1, Qi Ouyang2* and Jue Shi1* Abstract Background: The p53 pathway is differentially activated in response to distinct DNA damage, leading to alternative phenotypic outcomes in mammalian cells. Recent evidence suggests that p53 expression dynamics play an important role in the differential regulation of cell fate, but questions remain as to how p53 dynamics and the subsequent cellular response are modulated by variable DNA damage. Results: We identified a novel, bimodal switch of p53 dynamics modulated by DNA-damage strength that is crucial for cell-fate control. After low DNA damage, p53 underwent periodic pulsing and cells entered cell-cycle arrest. After high DNA damage, p53 underwent a strong monotonic increase and cells activated apoptosis. We found that the damage dose-dependent bimodal switch was due to differential Mdm2 upregulation, which controlled the alternative cell fates mainly by modulating the induction level and pro-apoptotic activities of p53. Conclusions: Our findings not only uncover a new mode of regulation for p53 dynamics and cell fate, but also suggest that p53 oscillation may function as a suppressor, maintaining a low level of p53 induction and pro-apoptotic activities so as to render cell-cycle arrest that allows damage repair. Background known to upregulate p53 by attenuating its interaction An efficient and precisely controlled DNA-damage re- with Mdm2, the E3 ubiquitin ligase that targets p53 for sponse is crucial for cell survival.
    [Show full text]
  • P53 Dynamics Vary Between Tissues and Are Linked with Radiation Sensitivity
    ARTICLE https://doi.org/10.1038/s41467-021-21145-z OPEN p53 dynamics vary between tissues and are linked with radiation sensitivity Jacob Stewart-Ornstein 1,5, Yoshiko Iwamoto2, Miles A. Miller 2, Mark A. Prytyskach2, Stephane Ferretti3, Philipp Holzer3, Joerg Kallen3, Pascal Furet3, Ashwini Jambhekar1, William C. Forrester 4, ✉ ✉ Ralph Weissleder1,2 & Galit Lahav 1 Radiation sensitivity varies greatly between tissues. The transcription factor p53 mediates the 1234567890():,; response to radiation; however, the abundance of p53 protein does not correlate well with the extent of radiosensitivity across tissues. Given recent studies showing that the temporal dynamics of p53 influence the fate of cultured cells in response to irradiation, we set out to determine the dynamic behavior of p53 and its impact on radiation sensitivity in vivo. We find that radiosensitive tissues show prolonged p53 signaling after radiation, while more resistant tissues show transient p53 activation. Sustaining p53 using a small molecule (NMI801) that inhibits Mdm2, a negative regulator of p53, reduced viability in cell culture and suppressed tumor growth. Our work proposes a mechanism for the control of radiation sensitivity and suggests tools to alter the dynamics of p53 to enhance tumor clearance. Similar approaches can be used to enhance killing of cancer cells or reduce toxicity in normal tissues following genotoxic therapies. 1 Department of Systems Biology and the Ludwig Center at Harvard, Blavatnik Institute at Harvard Medical School, Boston, MA, USA. 2 Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA. 3 Novartis Institutes for Biomedical Research, Basel, Switzerland. 4 Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
    [Show full text]
  • Dynamics of the DNA Damage Response: Insights from Live-Cell Imaging Ketki Karanam, Alexander Loewer and Galit Lahav
    Briefings in Functional Genomics Advance Access published January 4, 2013 BRIEFINGS IN FUNCTIONAL GENOMICS. page 1 of 9 doi:10.1093/bfgp/els059 Dynamics of the DNA damage response: insights from live-cell imaging Ketki Karanam, Alexander Loewer and Galit Lahav Abstract All organisms have to safeguard the integrity of their genome to prevent malfunctioning and oncogenic transform- ation. Sophisticated DNA damage response mechanisms have evolved to detect and repair genomic lesions. With the emergence of live-cell microscopy of individual cells, we now begin to appreciate the complex spatiotemporal kinetics of the DNA damage response and can address the causes and consequences of the heterogeneity in the responses of genetically identical cells. Here, we highlight key discoveries where live-cell imaging has provided unpre- cedented insights into how cells respond to DNA double-strand breaks and discuss the main challenges and promises in using this technique. Downloaded from Keywords: live-cell imaging; single cell; DNA damage; fluorescence microscopy; dynamics INTRODUCTION Modern medicine has exploited the DDR for The integrity of our genome is continually chal- cancer treatment [6]. Frontline therapies, such as http://bfg.oxfordjournals.org/ lenged by damaging agents such as reactive bypro- radiation and chemotherapy, function by generating ducts of cellular metabolism, background radiation high levels of DNA damage, often in the form of and environmental mutagens. Of the various types DSBs. Cancer cells are more susceptible to the of DNA lesions that arise within the cell, DNA adverse effects of DNA damage compared with double-strand breaks (DSBs) are particularly danger- healthy cells, as they frequently harbor mutations ous as their improper repair can cause chromosomal that compromise the DDR and cell cycle check- rearrangements that promote oncogenic transform- points.
    [Show full text]
  • Cell Systems 9, 548-558
    Article Inferring Leading Interactions in the p53/Mdm2/ Mdmx Circuit through Live-Cell Imaging and Modeling Graphical Abstract Authors Mathias L. Heltberg, Sheng-hong Chen, Alba Jime´ nez, Ashwini Jambhekar, Mogens H. Jensen, Galit Lahav Correspondence [email protected] (M.H.J.), [email protected] (G.L.) In Brief Heltberg et al. used mathematical modeling and live-cell imaging to distinguish between two possible functions of Mdmx in regulating the p53- Mdm2 network. Their results show a predominant role for Mdmx in suppressing Mdm2 activity in both unstressed cells and cells harboring DNA damage. Highlights d Impact factors discriminate between the dual functions of Mdmx in p53 regulation d The primary role of Mdmx is to enhance p53 degradation under non-stressed conditions d Mdmx suppression and DNA damage together regulate Mdm2-dependent p53 degradation Heltberg et al., 2019, Cell Systems 9, 548–558 December 18, 2019 ª 2019 Elsevier Inc. https://doi.org/10.1016/j.cels.2019.10.010 Cell Systems Article Inferring Leading Interactions in the p53/Mdm2/Mdmx Circuit through Live-Cell Imaging and Modeling Mathias L. Heltberg,1,2,4 Sheng-hong Chen,2,3,4 Alba Jime´ nez,2 Ashwini Jambhekar,2 Mogens H. Jensen,1,* and Galit Lahav2,5,* 1Niels Bohr Institute, University of Copenhagen 2100, Copenhagen, Denmark 2Department of Systems Biology, Harvard Medical School, Boston, MA, USA 3Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 4These authors contributed equally 5Lead Contact *Correspondence: [email protected] (M.H.J.), [email protected] (G.L.) https://doi.org/10.1016/j.cels.2019.10.010 SUMMARY logical outcomes.
    [Show full text]