Breast Cancer: Methods and Protocols

345 Pages·2016·11.577 MB·English

by  Jian Cao

Methods in
Molecular Biology 1406
Jian Cao Editor
Breast
Cancer
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

Breast Cancer
Methods and Protocols
Edited by
Jian Cao
School of Medicine, Stony Brook University, Stony Brook, NY, USA
Editor
Jian C ao
School of Medicine
Stony Brook University
Stony Brook, NY, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-3442-3 ISBN 978-1-4939-3444-7 (eBook)
DOI 10.1007/978-1-4939-3444-7
Library of Congress Control Number: 2015954358
Springer New York Heidelberg Dordrecht London
© Springer Science+Business Media New York 2 016
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is
concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction
on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation,
computer software, or by similar or dissimilar methodology now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not
imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and
regulations and therefore free for general use.
The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to
be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty,
express or implied, with respect to the material contained herein or for any errors or omissions that may have been made.
Printed on acid-free paper
Humana Press is a brand of Springer
Springer Science+Business Media LLC New York is part of Springer Science+Business Media (www.springer.com)
Prefa ce
The use of an appropriate method for studying or diagnosing breast cancer is imperative for
basic research and clinical practice. Although there are many books tackling breast cancer
on the market already, none are written systematically for the modern molecular biological
technologies spanning from basic research to clinical practice. The focus of this book is to
provide resources, ideas, and bench manuals for the study of breast cancer.
This book contains fi ve parts including methods used in clinical laboratory for diagnosis
(Detection of Molecular Markers of Breast Cancer), methods used in both clinical and research
laboratories for testing genetic alterations (Genetic Detection for Breast Cancer), methods
used to isolate breast cancer cells including circulating cancer cells and breast cancer stem cells
(Isolation of Breast Cancer Cells ), methods used to study the behavior of breast cancer cells
(In Vitro Experimental models for Breast Cancer), and methods used for mimicking human
breast cancer in a living organism (In Vivo Experimental Models for Breast Cancer). Each part
includes 3–11 different assays for readers to use based on their preferences. This book also
includes several recently developed techniques for the study of breast cancer progression.
Each chapter of this book was written by professionals who have extensive experience
on the corresponding techniques. Although most of these techniques can be found in the
published literature, the chapters described here are more comprehensive with detailed
step-by-step procedures so readers can successfully carry out the experiments without dif-
fi culty. In addition, extensive explanations for critical steps are described in the Notes sec-
tion of each chapter to ensure the successful completion of the experiments described.
These notes are usually essential for dependable results.
This book will be a valuable handbook for both graduate and advanced undergraduate
students of biological sciences as well as scientists, technicians, and physicians working in
the academic, hospital, or pharmaceutical industry aimed at studying or diagnosing breast
cancer. Our goal is to provide this book as a handbook for researchers who routinely work
on breast cancer research. I ask the readers to send any corrections or missing information
that can be revised in future editions.
Finally, I would like to thank the many authors for their thoughtful and timely contri-
butions. I also like to extend my appreciation to the Series Editor, Professor John Walker,
and the Springer staff, especially Dr. David Casey, for their contributions to the develop-
ment of this book.
I hope you fi nd this book to be valuable for your research.
Stony Brook, NY, USA J ian C ao, M.D.
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
PART I DETECTION OF MOLECULAR MARKERS OF BREAST CANCER
1 Basic Histopathological Methods and Breast Lesion Types for Research . . . . . 3
Nengtai O uyang and Lin W ang
2 C linical Applications for Immunohistochemistry of Breast Lesions. . . . . . . . . . 1 1
Kester H aye , Rajarsi Gupta , Christopher M etter , and Jingxuan Liu
3 Immunohistochemistry for Triple-Negative Breast Cancer. . . . . . . . . . . . . . . . 3 9
Kalnisha Naidoo and Sarah E . Pinder
4 I n Situ Hybridization of Breast Cancer Markers . . . . . . . . . . . . . . . . . . . . . . . 5 3
Li Min and Chengchao Shou
5 E valuation of Human Epidermal Growth Factor Receptor 2 (HER2) Gene
Status in Human Breast Cancer Formalin- Fixed Paraffin-Embedded (FFPE)
Tissue Specimens by Fluorescence In Situ Hybridization (FISH). . . . . . . . . . . 6 1
Harry C . Hwang and Allen M. G own
PART II GENETIC DETECTION FOR BREAST CANCER
6 Quantification of mRNA Levels Using Real-Time Polymerase Chain
Reaction (PCR) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3
Yiyi Li , K ai W ang , L onghua C hen , X iaoxia Zhu , and Jie Zhou
7 D etection of miRNA in Cultured Cells or Xenograft Tissues
of Breast Cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1
Martin Brown and M eiyun F an
8 P yrosequencing Analysis for Breast Cancer DNA Methylome . . . . . . . . . . . . . 8 9
Cem Kuscu and Canan K uscu
PART III ISOLATION OF BREAST CANCER CELLS
9 Vita-Assay™ Method of Enrichment and Identification of Circulating
Cancer Cells/Circulating Tumor Cells (CTCs) . . . . . . . . . . . . . . . . . . . . . . . . 1 07
Shaun T ulley , Qiang Zhao , Huan D ong , M ichael L. Pearl ,
and Wen-Tien Chen
10 Breast Cancer Stem Cell Isolation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Xuanmao Jiao , Albert A. R izvanov , Massimo C ristofanilli ,
Regina R . M iftakhova , and Richard G . P estell
vii
viii Contents
PART IV IN VITRO EXPERIMENTAL MODELS FOR BREAST CANCER
11 Cellular Apoptosis Assay of Breast Cancer. . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 39
Yu S un and W ei-Xing Z ong
12 A ssessment of Matrix Metalloproteinases by Gelatin Zymography . . . . . . . . . . 1 51
Jillian C athcart
13 A ssessment of Synthetic Matrix Metalloproteinase Inhibitors
by Fluorogenic Substrate Assay. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Ty J . Lively , D ale B. Bosco , Z ahraa I . K hamis , and Qing-Xiang A my Sang
14 Determination of Breast Cancer Cell Migratory Ability. . . . . . . . . . . . . . . . . . 1 71
David Schmitt , Joel A ndrews , and Ming T an
15 A Novel Collagen Dot Assay for Monitoring Cancer Cell Migration . . . . . . . . 1 81
Vincent M . Alford , E ric R oth , Qian Zhang , and Jian C ao
16 Three-Dimensional Assay for Studying Breast Cancer Cell Invasion. . . . . . . . . 1 89
Nikki A. Evensen
17 A Combined Phagocytosis and Fluorescent Substrate Degradation Assay
to Simultaneously Assess Cell Migration and Substrate Degradation . . . . . . . . 1 95
Ashleigh Pulkoski-Gross
18 A nalysis of Invadopodia Formation in Breast Cancer Cells. . . . . . . . . . . . . . . . 2 03
Ziqing Wang , Xiao L iang , Ming C ai , and Guangwei Du
19 Patient-Derived Tumor Xenograft Models of Breast Cancer. . . . . . . . . . . . . . . 2 11
Christopher D. S uarez and L aurie E. L ittlepage
20 M onitoring Phosphatidic Acid Signaling in Breast Cancer Cells
Using Genetically Encoded Biosensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 25
Maryia Lu , L i W ei R achel T ay , Jingquan H e , and Guangwei Du
21 3 D In Vitro Model for Breast Cancer Research Using Magnetic Levitation
and Bioprinting Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 39
Fransisca Leonard and Biana G odin
PART V IN VIVO EXPERIMENTAL MODELS FOR BREAST CANCER
22 Methods for Analyzing Tumor Angiogenesis in the Chick
Chorioallantoic Membrane Model. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Jacquelyn J . A mes , Terry Henderson , L ucy Liaw , and Peter C . Brooks
23 P harmacokinetics and Pharmacodynamics in Breast Cancer Animal Models. . . 2 71
Wei Wang , S ubhasree Nag , and Ruiwen Zhang
24 Intracellular Delivery of Fluorescently Labeled Polysaccharide
Nanoparticles to Cultured Breast Cancer Cells . . . . . . . . . . . . . . . . . . . . . . . . 289
Derek R ammelkamp , W eiyi L i , and Yizhi Meng
25 Imaging Matrix Metalloproteinase Activity Implicated in Breast
Cancer Progression. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
Gregg B. Fields and Maciej J. S tawikowski
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 31
Contributors
VINCENT M. ALFORD • Division of Cancer Prevention, Department of Medicine, S tony Brook
University , Stony Brook, N Y , U SA
JACQUELYN J. AMES • Center for Molecular Medicine, Maine Medical Center Research
Institute , S carborough, M E , U SA ; G raduate School of Biomedical Science
and Engineering, U niversity of Maine , Orono , ME, U SA
JOEL ANDREWS • Mitchell Cancer Institute , M obile, AL, U SA
DALE B. BOSCO • Institute of Molecular Biophysics, Florida State University , Tallahassee,
FL , USA
PETER C. BROOKS • Center for Molecular Medicine, M aine Medical Center Research
Institute , S carborough, ME, USA
MARTIN B ROWN • Departments of Pathology and Laboratory Medicine , U niversity
of Tennessee Health Science Center , Memphis , T N , U SA
MING CAI • Department of Integrative Biology and Pharmacology, T he University of Texas
Health Science Center at Houston , Houston, T X , U SA ; D epartment of General Surgery,
Union Hospital, Tongji Medical College, Huazhong University of Science and Technology ,
Wuhan , H ubei Province , China
JIAN CAO • Division of Cancer Prevention, Department of Medicine, S tony Brook University ,
Stony Brook, N Y , U SA
JILLIAN CATHCART • Department of Cellular and Molecular Pharmacology, Stony Brook
University , S tony Brook, NY, USA
LONGHUA CHEN • Department of Radiation Oncology, Nanfang Hospital, Southern
Medical University , G uangzhou, C hina
WEN-TIEN CHEN • Vitatex Inc. , Stony Brook, NY , U SA ; D ivision of Gynecologic Oncology ,
Stony Brook Medicine , S tony Brook, NY, USA
MASSIMO CRISTOFANILLI • Department of Cancer Biology, Sidney Kimmel Cancer Center,
Thomas Jefferson University , Philadelphia, P A, USA
HUAN D ONG • Vitatex Inc. , Stony Brook, NY , U SA
GUANGWEI DU • Department of Integrative Biology and Pharmacology, T he University
of Texas Health Science Center at Houston , H ouston, T X , U SA
NIKKI A. E VENSEN • Department of Pediatrics, NYU Medical School , N ew York , NY , U SA
MEIYUN F AN • Departments of Pathology and Laboratory Medicine , University of Tennessee
Health Science Center , Memphis, TN, USA
GREGG B. F IELDS • Department of Chemistry & Biochemistry , F lorida Atlantic University ,
Jupiter , F L , U SA ; Department of Chemistry , The Scripps Research Institute/Scripps
Florida , Jupiter, FL, USA ; Departments of Chemistry and Biology , T orrey Pines Institute
for Molecular Studies , Port St. Lucie, FL, USA
BIANA GODIN • Department of Nanomedicine, Houston Methodist Research Institute ,
Houston, T X, U SA
ALLEN M . G OWN • Department of Molecular Pathology, P henoPath Laboratories , Seattle,
WA, USA
RAJARSI GUPTA • Department of Pathology, Stony Brook University Hospital , S tony Brook,
NY, U SA
ix