Oncogene-Induced Senescence: Methods and Protocols

219 Pages·2017·7.354 MB·English

by  Mikhail A. Nikiforov (eds.)

Methods in
Molecular Biology 1534
Mikhail A. Nikiforov Editor
Oncogene-
Induced
Senescence
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB , UK
For further volumes:
http://www.springer.com/series/7651
Oncogene-Induced Senescence
Methods and Protocols
Edited by
Mikhail A. Nikiforov
Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
Editor
Mikhail A. Nikiforov
Department of Cell Stress Biology
Roswell Park Cancer Institute
Buffalo, NY, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-6668-4 ISBN 978-1-4939-6670-7 (eBook)
DOI 10.1007/978-1-4939-6670-7
Library of Congress Control Number: 2016955246
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Prefa ce
Oncogene-induced senescence is a multistep program triggered in response to aberrant
oncoprotein expression and/or activation. The eventual function of this fail-safe mecha-
nism is the suppression of the proliferation of cells at the preneoplastic stage ultimately
resulting in the prevention of fully malignant progeny. On the other hand, senescent cells
have been shown to promote cancer initiation and progression in several mouse models.
Since the discovery of oncogene-induced senescence in 1997 by Serrano et al., many
outstanding researchers have been working on this intriguing set of phenotypes. In addi-
tion to proliferation arrest, cells undergoing oncogene-induced senescence have been ini-
tially characterized by changes in the activity of senescence-associated β-galactosidase, cell
size, chromatin structure, histone modifi cations, DNA integrity, etc.
During the past two decades, new approaches for studying cellular processes underly-
ing senescence-associated phenotypes have emerged leading to the identifi cation of a num-
ber of genes that were implicated in the control and/or implementation of oncogene-induced
senescence. And yet markers of senescence that can be universally applied to all experimen-
tal systems have not been identifi ed and might not even exist. Conversely, there are virtually
no markers that are specifi c only to the cells undergoing oncogene-induced senescence.
Therefore, the analysis of phenotypes associated with oncogene-induced senescence
requires multiple approaches. This book offers in a single volume a unique collection of the
state-of-the-art experimental procedures utilized for the induction, detection, and model-
ing of this complex cellular program. The book encompasses protocols for studying
oncogene-i nduced senescence in human specimens and a variety of experimental models
including cultured mammalian cells, laboratory mice, and Drosophila m elanogaster . It also
offers a description of high-throughput approaches.
The book represents a useful asset for the wide audience of medical oncologists and
researchers in the fi elds of oncology, molecular and cellular biology, biochemistry, and ani-
mal development. The chapters are organized to provide step-by-step guides for experi-
mental procedures including the list of required reagents, equipment, and materials. Special
attention is paid to the appropriate controls and troubleshooting.
I would like to thank all the authors whose dedicated work made this book possible,
Brittany C. Lipchick, Leslie M. Paul-Rosner, and my colleagues at Roswell Park Cancer
Institute, and the Series Editor, Dr. John M. Walker, for their invaluable help in editing
this book.
Buffalo, NY, USA Mikhail A. Nikiforov
v
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 T he Immortal Senescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Anna Bianchi-Smiraglia , B rittany C. Lipchick , and Mikhail A. Nikiforov
2 S enescence Phenotypes Induced by Ras in Primary Cells. . . . . . . . . . . . . . . . . 1 7
Lena Lau and Gregory David
3 C ellular Model of p21-Induced Senescence. . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Michael Shtutman , B ey-Dih Chang , G ary P. Schools , and Eugenia V. Broude
4 D etecting Markers of Therapy-Induced Senescence in Cancer Cells. . . . . . . . . 4 1
Dorothy N. Y. Fan and Clemens A. Schmitt
5 G enome-Wide miRNA Screening for Genes Bypassing Oncogene-Induced
Senescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3
Maria V. Guijarro and Amancio Carnero
6 D etection of Dysfunctional Telomeres in Oncogene-Induced Senescence . . . . 6 9
Priyanka L. Patel and Utz Herbig
7 R T-qPCR Detection of Senescence-Associated Circular RNAs. . . . . . . . . . . . . 7 9
Amaresh C. Panda , K otb Abdelmohsen , and Myriam Gorospe
8 A utophagy Detection During Oncogene-Induced Senescence
Using Fluorescence Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Masako Narita and Masashi Narita
9 D etecting the Senescence-Associated Secretory Phenotype (SASP)
by High Content Microscopy Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Priya Hari and Juan Carlos Acosta
10 S udan Black B, The Specific Histochemical Stain for Lipofuscin:
A Novel Method to Detect Senescent Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Konstantinos Evangelou and Vassilis G. Gorgoulis
11 U sing [U-1 3 C6 ]-Glucose Tracer to Study Metabolic Changes
in Oncogene-Induced Senescence Fibroblasts . . . . . . . . . . . . . . . . . . . . . . . . . 1 21
Katerina I. Leonova and David A. Scott
12 D etection of the Ubiquitinome in Cells Undergoing
Oncogene-Induced Senescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Hengrui Zhu , L inh Le , H sin-Yao Tang , D avid W. Speicher ,
and Rugang Zhang
13 D etection of Reactive Oxygen Species in Cells Undergoing
Oncogene-Induced Senescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Rabii Ameziane-El-Hassani and Corinne Dupuy
vii
viii Contents
14 D etection of Senescent Cells by Extracellular Markers
Using a Flow Cytometry-Based Approach. . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Mohammad Althubiti and Salvador Macip
15 M etabolic Changes Investigated by Proton NMR Spectroscopy
in Cells Undergoing Oncogene-Induced Senescence. . . . . . . . . . . . . . . . . . . . 155
Claudia Gey and Karsten Seeger
16 D etection of Nucleotide Disbalance in Cells Undergoing Oncogene-Induced
Senescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 65
Mikhail A. Nikiforov and Donna S. Shewach
17 S enescence-Like Phenotypes in Human Nevi. . . . . . . . . . . . . . . . . . . . . . . . . . 175
Andrew Joselow , D arren Lynn , T amara Terzian , and Neil F. Box
18 D etection of Oncogene-Induced Senescence In Vivo . . . . . . . . . . . . . . . . . . . 1 85
Kwan-Hyuck Baek and Sandra Ryeom
19 D etection of Senescence Markers During Mammalian
Embryonic Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 99
M ekayla Storer and William M. Keyes
20 I nduction and Detection of Oncogene-Induced Cellular Senescence
in Drosophila . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Mai Nakamura and Tatsushi Igaki
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 19
Contributors
KOTB ABDELMOHSEN • Laboratory of Genetics and Genomics, N ational Institute on Aging-
Intramural Research Program, National Institutes of Health , B altimore, M D , U SA
JUAN CARLOS ACOSTA • Edinburgh Cancer Research UK Centre, Institute of Genetics
and Molecular Medicine, U niversity of Edinburgh , E dinburgh, U K
MOHAMMAD ALTHUBITI • Mechanisms of Cancer and Aging Laboratory , D epartment of
Molecular and Cell Biology , U niversity of Leicester, Leicester, U K ; C ancer Research UK
Leicester Centre , L eicester, U K ; D epartment of Biochemistry , F aculty of Medicine, Umm
Al-Qura University, M ecca, S audi Arabia
RABBII AMEZIANE-EL-HASSANI • UMR 8200, CNRS , V illejuif, F rance ; I nstitut Gustave
Roussy , V illejuif, F rance ; U nité de Biologie et de Recherche Médicale, C entre National de
l’Energie, des Sciences et des Techniques Nucléaires , R abat , M orocco
KWAN-HYUCK BAEK • Department of Molecular and Cellular Biology, Samsung Biomedical
Research Institute, S ungkyunkwan University School of Medicine , S uwon , G yeonggi,
Republic of Korea
ANNA BIANCHI-SMIRAGLIA • Department of Cell Stress Biology , R oswell Park Cancer
Institute , B uffalo, N Y , U SA
NEIL F. BOX • Department of Dermatology, U niversity of Colorado , A urora , C O , U SA ;
Charles C. Gates Center for Regenerative Medicine, University of Colorado,
Aurora, USA
EUGENIA V. BROUDE • Department of Drug Discovery and Biomedical Sciences, South
Carolina College of Pharmacy , U niversity of South Carolina , C olumbia, S C , U SA
AMANCIO CARNERO • Molecular Biology of Cancer Group, Oncohematology and Genetic
Department , I nstituto de Biomedicina de Sevilla (IBIS/HUVR/CSIC/Universidad de
Sevilla) , S evilla , S pain
BEY-DIH CHANG • PeptiMed, Inc. , M adison, W I , U SA
GREGORY DAVID • Department of Biochemistry and Molecular Pharmacology, Perlmutter
Cancer Institute, N ew York University School of Medicine , N ew York, N Y , U SA
CORINNE DUPUY • UMR 8200, CNRS , V illejuif, F rance ; I nstitut Gustave Roussy , V illejuif,
France ; U niversity Paris-Saclay , O rsay , F rance
KONSTANTINOS EVANGELOU • Molecular Carcinogenesis Group, Department of Histology
and Embryology, Medical School , N ational and Kapodistrian University of Athens ,
Athens, G reece
DOROTHY N.Y. FAN • Department of Hematology, Oncology and Tumor Immunology,
Campus Virchow Clinic , C harité—University Medical Center , B erlin, G ermany
CLAUDIA GEY • Institute of Chemistry , U niversity of Lübeck , L übeck, G ermany
VASSILIS G. GORGOULIS • Molecular Carcinogenesis Group, Department of Histology and
Embryology, Medical School , N ational and Kapodistrian University of Athens , A thens,
Greece ; B iomedical Research Foundation, A cademy of Athens , A thens, G reece ; F aculty of
Biology, Medicine and Health Manchester Cancer Research Centre, Manchester Academic
Health Sciences Centre , U niversity of Manchester , M anchester, U K
ix
x Contributors
MYRIAM GOROSPE • Laboratory of Genetics, N ational Institute on Aging-Intramural
Research Program, National Institutes of Health , B altimore, M D , U SA
MARIA V. GUIJARRO • Musculoskeletal and Oncology Lab, Department of Orthopaedics
and Rehabilitation, U niversity of Florida , G ainesville, F L, U SA
PRIYA HARI • Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular
Medicine, U niversity of Edinburgh , E dinburgh, U K
UTZ HERBIG • Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey
Medical School-Cancer Center, Rutgers Biomedical and Health Sciences , Newark , NJ , USA
TATSUSHI IGAKI • Laboratory of Genetics, Graduate School of Biostudies, K yoto University ,
Kyoto, J apan ; P RESTO , J apan Science and Technology Agency (JST) , S aitama, J apan
ANDREW JOSELOW • Charles C. Gates Center for Regenerative Medicine, U niversity of
Colorado , A urora , C O , U SA ; D epartment of Dermatology, U niversity of Colorado ,
Aurora , C O , U SA ; S chool of Medicine, T ulane University , N ew Orleans, L A , U SA
WILLIAM M. KEYES • Centre for Genomic Regulation (CRG), T he Barcelona Institute of
Science and Technology , B arcelona, S pain ; U niversitat Pompeu Fabra (UPF) , B arcelona,
Spain
LENA LAU • Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer
Institute, N ew York University School of Medicine , N ew York, N Y , U SA
LINH LE • Gene Expression and Regulation Program, T he Wistar Institute , P hiladelphia,
PA, U SA ; C ell and Molecular Biology Graduate Group, Perelman School of Medicine of
the University of Pennsylvania , P hiladelphia, P A, U SA
KATERINA I. LEONOVA • Department of Cell Stress Biology , R oswell Park Cancer Institute ,
Buffalo, N Y , U SA
BRITTANY C. LIPCHICK • Department of Cell Stress Biology , R oswell Park Cancer Institute ,
Buffalo, N Y , U SA
DARREN LYNN • Charles C. Gates Center for Regenerative Medicine, U niversity of
Colorado , A urora , C O , U SA ; D epartment of Dermatology, U niversity of Colorado ,
Aurora , C O , U SA
SALVADOR MACIP • Mechanisms of Cancer and Aging Laboratory, Department of Molecular
and Cell Biology, U niversity of Leicester , L eicester, U K ; C ancer Research UK Leicester
Centre , L eicester, U K
MAI NAKAMURA • Laboratory of Genetics, Graduate School of Biostudies, K yoto University ,
Kyoto, J apan
MASAKO NARITA • Cancer Research UK Cambridge Institute, U niversity of Cambridge ,
Cambridge, U K
MASASHI NARITA • Cancer Research UK Cambridge Institute, U niversity of Cambridge ,
Cambridge, U K
MIKHAIL A. NIKIFOROV • Department of Cell Stress Biology , R oswell Park Cancer Institute ,
Buffalo, N Y , U SA
AMARESH C. PANDA • Laboratory of Genetics and Genomics, N ational Institute on Aging-
Intramural Research Program, National Institutes of Health , B altimore, M D , U SA
PRIYANKA L. PATEL • Department of Microbiology, Biochemistry and Molecular Genetics,
New Jersey Medical School-Cancer Center , R utgers Biomedical and Health Sciences ,
Newark, N J , U SA
SANDRA RYEOM • Department of Cancer Biology, Abramson Family Cancer Research
Institute, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
CLEMENS A. SCHMITT • Department of Hematology, Oncology and Tumor Immunology,
Campus Virchow Clinic , C harité—University Medical Center , B erlin, G ermany ;
Contributors xi
Molekulares Krebsforschungszentrum—MKFZ , B erlin, G ermany ; M ax-Delbrück-Center
for Molecular Medicine , B erlin, G ermany ; M ax-Delbrück-Center for Molecular Medicine,
Berlin, Germany
GARY P. SCHOOLS • Department of Drug Discovery and Biomedical Sciences, South
Carolina College of Pharmacy , U niversity of South Carolin , C olumbia, S C , U SA
DAVID A. SCOTT • Department of Cell Stress Biology , R oswell Park Cancer Institute ,
Buffalo, N Y , U SA
KARSTEN SEEGAR • Institute of Chemistry , U niversity of Lübeck , L übeck, G ermany
DONNA S. SHEWACH • Department of Pharmacology , U niversity of Michigan , A nn Arbor,
MI , U SA
MICHAEL SHTUTMAN • Department of Drug Discovery and Biomedical Sciences, South
Carolina College of Pharmacy , U niversity of South Carolin , C olumbia, S C , U SA
DAVID W. SPEICHER • Molecular and Cellular Oncology Program and Proteomics Core,
The Wistar Institute , P hiladelphia, P A, U SA
MEKAYLA STORER • Centre for Genomic Regulation (CRG), T he Barcelona Institute of
Science and Technology , B arcelona, S pain ; U niversitat Pompeu Fabra (UPF) , B arcelona,
Spain ; P rogram in Neurosciences and Mental Health , H ospital for Sick Children ,
Toronto , O N , C anada
HSIN-YAO TANG • Molecular and Cellular Oncology Program and Proteomics Core,
The Wistar Institute , P hiladelphia, P A, U SA
TAMARA TERZIAN • Charles C. Gates Center for Regenerative Medicine, U niversity of
Colorado , A urora , C O , U SA ; D epartment of Dermatology, U niversity of Colorado ,
Aurora , C O , U SA
RUGANG ZHANG • Gene Expression and Regulation Program, T he Wistar Institute ,
Philadelphia, P A, U SA
HENGRUI ZHU • Gene Expression and Regulation Program, T he Wistar Institute ,
Philadelphia, P A, U SA