Hematopoietic Stem Cell Protocols

361 Pages·2014·7.93 MB·English

by  Kevin D. Bunting, Cheng-Kui Qu (eds.)

Methods in
Molecular Biology 1185
Kevin D. Bunting
Cheng-Kui Qu Editors
Hematopoietic
Stem Cell
Protocols
Third Edition
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
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Hematopoietic Stem Cell
Protocols
Third Edition
Edited by
Kevin D. Bunting and Cheng-Kui Qu
Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine,
Atlanta, GA, USA
Editors
Kevin D. Bunting Cheng-Kui Qu
Department of Pediatrics Department of Pediatrics
Aflac Cancer and Blood Disorders Center Aflac Cancer and Blood Disorders Center
Emory University School of Medicine Emory University School of Medicine
Atlanta, GA, USA Atlanta, GA, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-1132-5 ISBN 978-1-4939-1133-2 (eBook)
DOI 10.1007/978-1-4939-1133-2
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Preface
The hematopoietic stem cell (HSC) fi eld has continued to grow and become more sophis-
ticated with each passing year. Methods for isolation of HSC and progenitor subsets and a
variety of single cell and molecular technologies have led to a greater understanding of the
heterogeneity within the phenotypically defi ned HSC subsets. The fi rst two editions of
Hematopoietic Stem Cell Protocols are very thorough resources in the user-friendly Methods
in Molecular Medicine format. This is the third edition of Hematopoietic Stem Cell Protocols
and aims to provide timely protocols in the HSC fi eld while continuing the tradition. This
edition teaches major new technologies that have advanced the state of the art in the fi eld
and promise to drive research in many unexpected and exciting ways in the future.
The fi rst chapter is an overview that ties the other chapters together into a larger picture
of the HSC landscape.
The methods chapters include similar categories to the last editions but with entirely
new approaches and innovative insights. The author list is made up of leading researchers
who have made major contributions toward these technical advances and who have pro-
vided a much needed resource for new stem cell investigators.
We thank all of the contributors for their time and effort. It has been a pleasure for both
co-editors to work with the contributing authors on this project. To provide updates in the
fast paced HSC fi eld is an important endeavor. We have specifi cally focused on the HSC
population and did not focus directly on the stem cell-associated niche which comprises a
new fi eld in itself and deserving of a separate edition. We are delighted to have organized
this information into a comprehensive and essential resource. It is our hope that this
resource will be a critical addition to all laboratories seeking to isolate and characterize
HSCs for research and for therapeutic applications.
Atlanta, GA, USA Kevin D. Bunting, Ph.D.
Cheng-Kui Qu, M.D., Ph.D.
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
PART I OVERVIEW
1 The Hematopoietic Stem Cell Landscape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Kevin D. Bunting and Cheng-Kui Qu
PART II STEM CELL ENRICHMENT AND HETEROGENEITY
2 Investigating the Interaction Between Hematopoietic Stem Cells
and Their Niche During Embryonic Development: Optimizing
the Isolation of Fetal and Newborn Stem Cells From Liver, Spleen,
and Bone Marrow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Huimin Cao, Brenda Williams, and Susan K. Nilsson
3 Single-Cell PCR Profiling of Gene Expression in Hematopoiesis. . . . . . . . . . . . 21
José Teles, Tariq Enver, and Cristina Pina
4 Hematopoietic Stem and Progenitor Cell Mobilization in Mice. . . . . . . . . . . . . 43
Jonathan Hoggatt, Tiffany A. Tate, and Louis M. Pelus
5 Cell Cycle Measurement of Mouse Hematopoietic
Stem/Progenitor Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Brahmananda Reddy Chitteti and Edward F. Srour
6 Flow Cytometric Analysis of Signaling and Apoptosis
in Hematopoietic Stem Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Lei Dong and Cheng-Kui Qu
PART III MOLECULAR AND CELLULAR CHARACTERIZATION
7 Gene Expression Profiling of Hematopoietic Stem Cells (HSCs). . . . . . . . . . . . 91
Nalini Raghavachari
8 Measuring MicroRNA Expression in Mouse Hematopoietic Stem Cells. . . . . . . 121
Wenhuo Hu and Christopher Y. Park
9 DNA Methylation Profiling of Hematopoietic Stem Cells . . . . . . . . . . . . . . . . . 141
Amber Hogart Begtrup
10 Metabolic Characterization of Hematopoietic Stem Cells . . . . . . . . . . . . . . . . . 155
Fatih Kocabas, Junke Zheng, Chengcheng Zhang,
and Hesham A. Sadek
11 Nanoproteomic Assays on Hematopoietic Stem Cells . . . . . . . . . . . . . . . . . . . . 165
Heath L. Bradley, Himalee Sabnis, Deborah Pritchett,
and Kevin D. Bunting
vii
viii Contents
PART IV IN VITRO ASSAYS AND DIFFERENTIATION
12 Hematopoietic Differentiation of Pluripotent Stem Cells in Culture . . . . . . . . . 181
Jason A. Mills, Prasuna Paluru, Mitchell J. Weiss,
Paul Gadue, and Deborah L. French
13 Ex Vivo Assays to Study Self-Renewal, Long-Term Expansion,
and Leukemic Transformation of Genetically Modified Human
Hematopoietic and Patient-Derived Leukemic Stem Cells. . . . . . . . . . . . . . . . . 195
Pallavi Sontakke, Marco Carretta, Marta Capala,
Hein Schepers, and Jan Jacob Schuringa
14 Ex Vivo Expansion of Murine and Human Hematopoietic Stem Cells. . . . . . . . 211
Phuong L. Doan and John P. Chute
15 Using Microfluidics to Investigate Hematopoietic Stem Cell
and Microniche Interactions at the Single Cell Level. . . . . . . . . . . . . . . . . . . . . 223
Byungwook Ahn, Zhengqi Wang, David R. Archer,
and Wilbur A. Lam
PART V TRANSPLANTATION ASSAYS AND IMAGING ENGRAFTMENT
16 Five-Lineage Clonal Analysis of Hematopoietic Stem/Progenitor Cells. . . . . . . 237
Ryo Yamamoto, Yohei Morita, and Hiromitsu Nakauchi
17 Intravital Imaging of Hematopoietic Stem Cells in the Mouse Skull. . . . . . . . . . 247
Juwell W. Wu, Judith M. Runnels, and Charles P. Lin
18 Immunodeficient Mouse Model for Human Hematopoietic
Stem Cell Engraftment and Immune System Development . . . . . . . . . . . . . . . . 267
Ken-Edwin Aryee, Leonard D. Shultz, and Michael A. Brehm
19 Homing and Migration Assays of Hematopoietic Stem/Progenitor Cells. . . . . . 279
Xi C. He, Zhenrui Li, Rio Sugimura, Jason Ross, Meng Zhao,
and Linheng Li
PART VI GENETIC MODIFICATION
20 Retroviral Transduction of Murine and Human Hematopoietic
Progenitors and Stem Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
Marioara F. Ciuculescu, Christian Brendel, Chad E. Harris,
and David A. Williams
21 Lentiviral Gene Transduction of Mouse and Human Hematopoietic
Stem Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
Niek P. van Til and Gerard Wagemaker
22 High-Throughput Genomic Mapping of Vector Integration Sites
in Gene Therapy Studies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
Brian C. Beard, Jennifer E. Adair, Grant D. Trobridge,
and Hans-Peter Kiem
23 Barcoded Vector Libraries and Retroviral or Lentiviral Barcoding
of Hematopoietic Stem Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
Leonid V. Bystrykh, Gerald de Haan, and Evgenia Verovskaya
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361
Contributors
JENNIFER E. A DAIR • Fred Hutchinson Cancer Research Center, U niversity of Washington
School of Medicine, Seattle , W A , U SA
BYUNGWOOK AHN • Department of Pediatrics, Afl ac Cancer and Blood Disorders Center,
Emory University School of Medicine, A tlanta , G A , USA
DAVID R. A RCHER • Division of Hem/Onc/BMT, Department of Pediatrics, Afl ac Cancer
and Blood Disorders Center , Emory University School of Medicine, A tlanta, GA , U SA
KEN-EDWIN ARYEE • Program in Molecular Medicine, U niversity of Massachusetts Medical
School, Worcester, MA, USA
BRIAN C . BEARD • Fred Hutchinson Cancer Research Center, S eattle , W A , U SA
AMBER H . BEGTRUP • Division of Human Genetics, Department of Pediatrics, College of
Medicine, Cincinnati Children’s Research Hospital Medical Center, Cincinnati, OH, USA
HEATH L. B RADLEY • Division of Hem/Onc/BMT, Department of Pediatrics, A fl ac Cancer
and Blood Disorders Center, Emory University School of Medicine , A tlanta, GA , U SA
MICHAEL A. BREHM • Program of Molecular Medicine, U niversity of Massachusetts Medical
School, W orcester , M A , U SA
CHRISTIAN B RENDEL • Boston Children’s Hospital and Dana Farber Cancer Institute,
Harvard Medical School, Boston, MA, USA
KEVIN D. B UNTING • Department of Pediatrics, Afl ac Cancer and Blood Disorders Center,
Emory University School of Medicine, Atlanta , G A , U SA
LEONID V. B YSTRYKH • Laboratory of Ageing Biology and Stem Cells, European Research
Institute for the Biology of Ageing, University Medical Centre Groningen, University
of Groningen , G roningen , The Netherlands
HUIMIN CAO • CMSE , C ommonwealth Scientifi c and Industrial Research Organization
(CSIRO), C layton, Australia
MARTA CAPALA • Department of Experimental Hematology , U niversity Medical Center
Groningen, University of Groningen , Groningen , T he Netherlands
MARCO CARRETTA • Department of Experimental Hematology , University Medical Center
Groningen, University of Groningen , G roningen , T he Netherlands
BRAHMANANDA REDDY CHITTETI • Indiana University School of Medicine, Indianapolis,
IN, U SA
JOHN P . CHUTE • Division of Hem/Onc, Department of Medicine, University of California
Los Angeles, Los Angeles, USA
MARIOARA F. C IUCULESCU • Boston Children’s Hospital and Dana Farber Cancer Institute,
Harvard Medical School, Boston, MA, USA
PHUONG L. D OAN • Division of Hematologic Malignancies and Cellular Therapy, D uke
University Medical Center , D urham, NC, USA
LEI DONG • Division of Hem/Onc/BMT, Department of Pediatrics, Afl ac Cancer
and Blood Disorders Center, Emory , U niversity School of Medicine, A tlanta, GA , U SA
TARIQ E NVER • Stem Cell Laboratory , University College London Cancer Institute,
London, UK
ix