AP-1 Imprints a Reversible Transcriptional Program of Senescent Cells
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
Cellular Responses to Erbb-2 Overexpression in Human Mammary Luminal Epithelial Cells: Comparison of Mrna and Protein Expression
British Journal of Cancer (2004) 90, 173 – 181 & 2004 Cancer Research UK All rights reserved 0007 – 0920/04 $25.00 www.bjcancer.com Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression SL White1, S Gharbi1, MF Bertani1, H-L Chan1, MD Waterfield1 and JF Timms*,1 1 Ludwig Institute for Cancer Research, Wing 1.1, Cruciform Building, Gower Street, London WCIE 6BT, UK Microarray analysis offers a powerful tool for studying the mechanisms of cellular transformation, although the correlation between mRNA and protein expression is largely unknown. In this study, a microarray analysis was performed to compare transcription in response to overexpression of the ErbB-2 receptor tyrosine kinase in a model mammary luminal epithelial cell system, and in response to the ErbB-specific growth factor heregulin b1. We sought to validate mRNA changes by monitoring changes at the protein level using a parallel proteomics strategy, and report a surprisingly high correlation between transcription and translation for the subset of genes studied. We further characterised the identified targets and relate differential expression to changes in the biological properties of ErbB-2-overexpressing cells. We found differential regulation of several key cell cycle modulators, including cyclin D2, and downregulation of a large number of interferon-inducible genes, consistent with increased proliferation of the ErbB-2- overexpressing cells. Furthermore, differential expression of genes involved in extracellular matrix modelling and cellular adhesion was linked to altered adhesion of these cells. Finally, we provide evidence for enhanced autocrine activation of MAPK signalling and the AP-1 transcription complex. -
2017.08.28 Anne Barry-Reidy Thesis Final.Pdf
REGULATION OF BOVINE β-DEFENSIN EXPRESSION THIS THESIS IS SUBMITTED TO THE UNIVERSITY OF DUBLIN FOR THE DEGREE OF DOCTOR OF PHILOSOPHY 2017 ANNE BARRY-REIDY SCHOOL OF BIOCHEMISTRY & IMMUNOLOGY TRINITY COLLEGE DUBLIN SUPERVISORS: PROF. CLIONA O’FARRELLY & DR. KIERAN MEADE TABLE OF CONTENTS DECLARATION ................................................................................................................................. vii ACKNOWLEDGEMENTS ................................................................................................................... viii ABBREVIATIONS ................................................................................................................................ix LIST OF FIGURES............................................................................................................................. xiii LIST OF TABLES .............................................................................................................................. xvii ABSTRACT ........................................................................................................................................xix Chapter 1 Introduction ........................................................................................................ 1 1.1 Antimicrobial/Host-defence peptides ..................................................................... 1 1.2 Defensins................................................................................................................. 1 1.3 β-defensins ............................................................................................................. -
Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7 -
Cellular Senescence Promotes Skin Carcinogenesis Through P38mapk and P44/P42mapk Signaling
Author Manuscript Published OnlineFirst on July 8, 2020; DOI: 10.1158/0008-5472.CAN-20-0108 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Cellular senescence promotes skin carcinogenesis through p38MAPK and p44/p42 MAPK signaling Fatouma Alimirah1, Tanya Pulido1, Alexis Valdovinos1, Sena Alptekin1,2, Emily Chang1, Elijah Jones1, Diego A. Diaz1, Jose Flores1, Michael C. Velarde1,3, Marco Demaria1,4, Albert R. Davalos1, Christopher D. Wiley1, Chandani Limbad1, Pierre-Yves Desprez1, and Judith Campisi1,5* 1Buck Institute for Research on Aging, Novato, CA 94945, USA 2Dokuz Eylul University School of Medicine, Izmir 35340, Turkey 3Institute of Biology, University of the Philippines Diliman, College of Science, Quezon City 1101, Philippines 4European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, the Netherlands 5Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA *Lead Contact: Judith Campisi, Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA; Email: [email protected] or [email protected]. Telephone: 1-415-209-2066; Fax: 1-415-493-3640 Running title: Senescence and skin carcinogenesis Key words: doxorubicin, senescence-associated secretory phenotype, squamous cell carcinoma, microenvironment, inflammation, transgenic mice, tumorspheres Conflict of Interests JC is a co-founder of Unity Biotechnology and MD owns equity in Unity Biotechnology. All other authors declare no competing financial interests. Downloaded from cancerres.aacrjournals.org on September 25, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on July 8, 2020; DOI: 10.1158/0008-5472.CAN-20-0108 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. -
Cellular Senescence: Friend Or Foe to Respiratory Viral Infections?
Early View Perspective Cellular Senescence: Friend or Foe to Respiratory Viral Infections? William J. Kelley, Rachel L. Zemans, Daniel R. Goldstein Please cite this article as: Kelley WJ, Zemans RL, Goldstein DR. Cellular Senescence: Friend or Foe to Respiratory Viral Infections?. Eur Respir J 2020; in press (https://doi.org/10.1183/13993003.02708-2020). This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Copyright ©ERS 2020. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial Licence 4.0. Cellular Senescence: Friend or Foe to Respiratory Viral Infections? William J. Kelley1,2,3 , Rachel L. Zemans1,2 and Daniel R. Goldstein 1,2,3 1:Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA 2:Program in Immunology, University of Michigan, Ann Arbor, MI, USA 3:Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI USA Email of corresponding author: [email protected] Address of corresponding author: NCRC B020-209W 2800 Plymouth Road Ann Arbor, MI 48104, USA Word count: 2750 Take Home Senescence associates with fibrotic lung diseases. Emerging therapies to reduce senescence may treat chronic lung diseases, but the impact of senescence during acute respiratory viral infections is unclear and requires future investigation. Abstract Cellular senescence permanently arrests the replication of various cell types and contributes to age- associated diseases. -
Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol . -
Integration of 198 Chip-Seq Datasets Reveals Human Cis-Regulatory Regions
Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions Hamid Bolouri & Larry Ruzzo Thanks to Stephen Tapscott, Steven Henikoff & Zizhen Yao Slides will be available from: http://labs.fhcrc.org/bolouri/ Email [email protected] for manuscript (Bolouri & Ruzzo, submitted) Kleinjan & van Heyningen, Am. J. Hum. Genet., 2005, (76)8–32 Epstein, Briefings in Func. Genom. & Protemoics, 2009, 8(4)310-16 Regulation of SPi1 (Sfpi1, PU.1 protein) expression – part 1 miR155*, miR569# ~750nt promoter ~250nt promoter The antisense RNA • causes translational stalling • has its own promoter • requires distal SPI1 enhancer • is transcribed with/without SPI1. # Hikami et al, Arthritis & Rheumatism, 2011, 63(3):755–763 * Vigorito et al, 2007, Immunity 27, 847–859 Ebralidze et al, Genes & Development, 2008, 22: 2085-2092. Regulation of SPi1 expression – part 2 (mouse coordinates) Bidirectional ncRNA transcription proportional to PU.1 expression PU.1/ELF1/FLI1/GLI1 GATA1 GATA1 Sox4/TCF/LEF PU.1 RUNX1 SP1 RUNX1 RUNX1 SP1 ELF1 NF-kB SATB1 IKAROS PU.1 cJun/CEBP OCT1 cJun/CEBP 500b 500b 500b 500b 500b 750b 500b -18Kb -14Kb -12Kb -10Kb -9Kb Chou et al, Blood, 2009, 114: 983-994 Hoogenkamp et al, Molecular & Cellular Biology, 2007, 27(21):7425-7438 Zarnegar & Rothenberg, 2010, Mol. & cell Biol. 4922-4939 An NF-kB binding-site variant in the SPI1 URE reduces PU.1 expression & is GGGCCTCCCC correlated with AML GGGTCTTCCC Bonadies et al, Oncogene, 2009, 29(7):1062-72. SATB1 binding site A distal single nucleotide polymorphism alters long- range regulation of the PU.1 gene in acute myeloid leukemia Steidl et al, J Clin Invest. -
Immune Clearance of Senescent Cells to Combat Ageing and Chronic Diseases
cells Review Immune Clearance of Senescent Cells to Combat Ageing and Chronic Diseases Ping Song * , Junqing An and Ming-Hui Zou Center for Molecular and Translational Medicine, Georgia State University, 157 Decatur Street SE, Atlanta, GA 30303, USA; [email protected] (J.A.); [email protected] (M.-H.Z.) * Correspondence: [email protected]; Tel.: +1-404-413-6636 Received: 29 January 2020; Accepted: 5 March 2020; Published: 10 March 2020 Abstract: Senescent cells are generally characterized by permanent cell cycle arrest, metabolic alteration and activation, and apoptotic resistance in multiple organs due to various stressors. Excessive accumulation of senescent cells in numerous tissues leads to multiple chronic diseases, tissue dysfunction, age-related diseases and organ ageing. Immune cells can remove senescent cells. Immunaging or impaired innate and adaptive immune responses by senescent cells result in persistent accumulation of various senescent cells. Although senolytics—drugs that selectively remove senescent cells by inducing their apoptosis—are recent hot topics and are making significant research progress, senescence immunotherapies using immune cell-mediated clearance of senescent cells are emerging and promising strategies to fight ageing and multiple chronic diseases. This short review provides an overview of the research progress to date concerning senescent cell-caused chronic diseases and tissue ageing, as well as the regulation of senescence by small-molecule drugs in clinical trials and different roles and regulation of immune cells in the elimination of senescent cells. Mounting evidence indicates that immunotherapy targeting senescent cells combats ageing and chronic diseases and subsequently extends the healthy lifespan. Keywords: cellular senescence; senescence immunotherapy; ageing; chronic disease; ageing markers 1. -
Cellular Senescence and Inflammaging in the Skin Microenvironment
International Journal of Molecular Sciences Review Cellular Senescence and Inflammaging in the Skin Microenvironment Young In Lee 1,2 , Sooyeon Choi 1, Won Seok Roh 1 , Ju Hee Lee 1,2,* and Tae-Gyun Kim 1,* 1 Department of Dermatology, Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul 107-11, Korea; [email protected] (Y.I.L.); [email protected] (S.C.); [email protected] (W.S.R.) 2 Scar Laser and Plastic Surgery Center, Yonsei Cancer Hospital, Yonsei University College of Medicine, Seoul 107-11, Korea * Correspondence: [email protected] (J.H.L.); [email protected] (T.-G.K.); Tel.: +82-2-2228-2080 (J.H.L. & T.-G.K.) Abstract: Cellular senescence and aging result in a reduced ability to manage persistent types of inflammation. Thus, the chronic low-level inflammation associated with aging phenotype is called “inflammaging”. Inflammaging is not only related with age-associated chronic systemic diseases such as cardiovascular disease and diabetes, but also skin aging. As the largest organ of the body, skin is continuously exposed to external stressors such as UV radiation, air particulate matter, and human microbiome. In this review article, we present mechanisms for accumulation of senescence cells in different compartments of the skin based on cell types, and their association with skin resident immune cells to describe changes in cutaneous immunity during the aging process. Keywords: inflammaging; senescence; skin; fibroblasts; keratinocytes; melanocytes; immune cells Citation: Lee, Y.I.; Choi, S.; Roh, W.S.; Lee, J.H.; Kim, T.-G. Cellular Senescence and Inflammaging in the 1. -
Integrative Bulk and Single-Cell Profiling of Premanufacture T-Cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-Cell Therapy
Published OnlineFirst April 5, 2021; DOI: 10.1158/2159-8290.CD-20-1677 RESEARCH ARTICLE Integrative Bulk and Single-Cell Profiling of Premanufacture T-cell Populations Reveals Factors Mediating Long-Term Persistence of CAR T-cell Therapy Gregory M. Chen1, Changya Chen2,3, Rajat K. Das2, Peng Gao2, Chia-Hui Chen2, Shovik Bandyopadhyay4, Yang-Yang Ding2,5, Yasin Uzun2,3, Wenbao Yu2, Qin Zhu1, Regina M. Myers2, Stephan A. Grupp2,5, David M. Barrett2,5, and Kai Tan2,3,5 Downloaded from cancerdiscovery.aacrjournals.org on October 1, 2021. © 2021 American Association for Cancer Research. Published OnlineFirst April 5, 2021; DOI: 10.1158/2159-8290.CD-20-1677 ABSTRACT The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. -
Cellular Senescence and Apoptosis: How Cellular Responses Might Influence Aging Phenotypes
Experimental Gerontology 38 (2003) 5–11 www.elsevier.com/locate/expgero Cellular senescence and apoptosis: how cellular responses might influence aging phenotypes Judith Campisia,b,* aLife Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA bBuck Institute for Age Research, 8001 Redwood Blvd., Novato, CA 94945, USA Received 20 May 2002; accepted 28 May 2002 Abstract Aging in complex multi-cellular organisms such as mammals entails distinctive changes in cells and molecules that ultimately compromise the fitness of adult organisms. These cellular and molecular changes lead to the phenotypes we recognize as aging. This review discusses some of the cellular and molecular changes that occur with age, specifically changes that occur as a result of cellular responses that evolved to ameliorate the inevitable damage that is caused by endogenous and environmental insults. Because the force of natural selection declines with age, it is likely that these processes were never optimized during their evolution to benefit old organisms. That is, some age- related changes may be the result of gene activities that were selected for their beneficial effects in young organisms, but the same gene activities may have unselected, deleterious effects in old organisms, a phenomenon termed antagonistic pleiotropy. Two cellular processes, apoptosis and cellular senescence, may be examples of antagonistic pleiotropy. Both processes are essential for the viability and fitness of young organisms, but may contribute to aging phenotypes, including certain age-related diseases. q 2002 Elsevier Science Inc. All rights reserved. Keywords: Antagonistic pleiotropy; Apoptosis; Cancer; Cellular senescence; DNA damage response; Neurodegeneration; p53; Telomeres 1.