Functional Lipidomics 1st Edition
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Preface
With the sequencing of the genomes of model organisms, humans, pathogens, and
crops, the science of genomics paved the way for the systematic study of cellular
functions of encoded proteins. Beyond proteomics, however, is the realm of nonge-
netically encoded information encompassing lipids, carbohydrates, glycopeptides,
metabolic pathways, lipid–protein interactions, and more. The explosion of infor-
mation in the postgenomic era challenges science to be integrative, as well as
reductionist, in pursuing potential practical biomedical applications. Lipids, often
considered as just fats and oils, are essential elements in cell signaling and subcellular
structure. Scientists in the lipid research field have started to examine the discipline
on a broader scale and to extract knowledge and patterns of various lipids in a more
systematic way.
Systematically analyzing the lipidome provides opportunities for therapeutic
intervention and diagnosis. The expression patterns and levels of lipids and lipid-
binding proteins could be important markers of a developmental stage, pathological
condition, or disease treatment. Lipid metabolites may reveal biochemical patterns
related to disease states such as cancer, immune function, and neurodegenerative
disorders. Monitoring changes in the lipidome over time may lead to understanding
of the effects of disease, medication, diet, or environmental factors on lipid metab-
olism and phenotype. Modeling the differences of the lipid metabolic pathways in
prokaryotic versus mammalian cells and tissues may provide new targets for anti-
bacterial drug design. Simultaneous monitoring of all lipid species at basal level or
under stimulation may reveal cross-talk between major lipid-signaling pathways.
Comprehensive analysis of lipids may uncover novel lipid species at lower quantities.
By applying a systematic approach similar to that used for genomics and proteomics,
an integrated knowledge base can be developed for bacteria, yeast, and the human
lipidome. Such a knowledge base has the potential to identify and validate targets
for improved, personalized medicine and health.
In this edited volume, we intend to introduce the notion of “ functional lipidom-
ics,” by which we mean the total profiling of lipids and the entities that interact
functionally with lipids. We define the total lipid composition of a cell or organ as
the “lipidome.” Lipidomics can include the functional genomics of lipid metabolism,
i.e., understanding the biosynthetic pathways, the function and dysfunction of lipids,
biological membranes, lipoproteins, and protein–lipid interactions. The biosynthesis,
metabolism, and function of fatty acids, acylglyerols, glycerophospholipids, sphin-
golipids, terpenes including steroids, and lipids that form complexes with proteins
and sugars will be uncovered in this book. The state of the art of lipid analysis
approaches, diagnostics using lipid and lipid-binding protein patterns, and the ther-
apeutic significance in targeting proteins involved with the lipid-signaling pathway
will be elaborated from both academic and industrial perspectives.
We have presented topics at the forefront of current lipid research as viewed by
an international set of authors from the United States, Europe, Canada, Singapore,
and China. Our purpose was threefold: first, we hoped to capture the first snapshot
of the current state of the art in functional lipidomics. Second, we wished to provide
a comprehensive background for scientists new to the field and whose contributions
will propel further understanding of lipidomics and biology. Finally, this monograph
may serve as a resource for developing didactic courses in lipid cell signaling and
lipid bioinformatics that could be employed for graduate study.
About the Authors
Li Feng
Li Feng is a scientist at Echelon Biosciences, Inc., an Aeterna-Zentaris Company,
a leader in the field of lipid cell signaling research and product development. She
earned her [Link]. and [Link]. in chemistry from Beijing University and a Ph.D. in
medicinal chemistry from the University of Utah in 1999, followed by two years as
a postdoctoral research associate at the Center for Cell Signaling, University of Utah.
She has been involved in the technology development that furthered the growth of
Echelon and facilitated research in the lipid signaling research field. Her research
projects and interests include (1) reagents and assay development for lipid signaling
research, (2) anticancer drug development targeting lipid-metabolizing enzymes, and
(3) development of platform technology for profiling the interactions of lipids and
lipid-associated proteins.
Glenn D. Prestwich
Glenn D. Prestwich, Presidential Professor of Medicinal Chemistry at the University
of Utah since 1996, holds concurrent adjunct appointments in the departments of
chemistry, biochemistry, and bioengineering. He is the director for two Utah “Centers
of Excellence” for technology commercialization: the Center for Cell Signaling and
the Center for Therapeutic Biomaterials. He chaired the University of Utah Depart-
ment of Medicinal Chemistry from 1996 to 2002, and is currently program leader
of the Molecular Pharmacology Program of the Huntsman Cancer Institute. Until
its aquisition by Aeterna-Zentaris in 2005, he was the Chief Scientific Officer,
Echelon Biosciences, Inc. (Salt Lake City, Utah), which he cofounded in 1997. In
addition, he serves as Chief Scientific Officer, Sentrx Surgical, Inc. (Salt Lake City,
Utah), a new therapeutic biomaterials start-up, which he cofounded in 2004. His
research programs now include (1) new reagents for lipid signaling in cell biology,
(2) anticancer drugs and diagnostics, and (3) biomaterials for wound repair, cartilage
repair, tissue engineering, and prevention of postsurgical adhesions.
Dr. Prestwich graduated with a [Link]. (honors) in chemistry from the California
Institute of Technology in 1970. He earned a Ph.D. in chemistry from Stanford
University in 1974, followed by three years as an NIH postdoctoral fellow, first at
Cornell University and then at the International Centre for Insect Physiology and
Ecology in Nairobi, Kenya. From 1977 to 1996, he was at Stony Brook University
in Stony Brook, New York, as professor of chemistry, professor of biochemistry and
cell biology, and director of the New York State Center for Advanced Technology
in Medical Biotechnology. He cofounded Clear Solutions Biotechnology, Inc. (Stony
Brook), to commercialize biomaterials derived from hyaluronic acid. He is a recip-
ient of the Alfred P. Sloan Research and Dreyfus Teacher–Scholar awards and was
honored with the 1998 Paul Dawson Biotechnology Award of the American Asso-
ciation of Colleges of Pharmacy.
Dr. Prestwich has published over 490 technical papers and book chapters, includ-
ing popular articles in National Geographic and Scientific American. Over 28 years,
he has trained more than 66 graduate students and 52 postdoctoral scientists. He is
an inventor on over 40 patents and patent applications, including the enabling
technologies for his four start-up companies.
List of Contributors
Michelle D. Armstrong
The Alliance for Cellular Signaling Lipidomics Laboratory
Department of Pharmacology and the Institute for Chemical Biology
Vanderbilt University Medical Center
Nashville, Tennessee
Robert M. Barkley
Department of Pharmacology
University of Colorado Health Sciences Center
Aurora, Colorado
Rebecca C. Bowers–Gentry
University of California, San Diego
Department of Chemistry and Biochemistry and Department of Pharmacology
La Jolla, California
H. Alex Brown
Department of Pharmacology
Vanderbilt University Medical Center
Nashville, Tennessee
Pietro De Camilli
Howard Hughes Medical Institute
Department of Cell Biology
Yale University School of Medicine
Boyer Center for Molecular Medicine
New Haven, Connecticut
Leena Chakravarty
Kwai Wa Cheng
Department of Molecular Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
David Crotzer
Department of Gynecologic Oncology
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Luciano De Petrocellis
Istituto di Cibernetica “Eduardo Caianiello”
Consiglio Nazionale delle Ricerche Pozzuoli (Napoli), Italy
Raymond A. Deems
Department of Chemistry and Biochemistry
University of California, San Diego
La Jolla, California
Edward A. Dennis
Department of Chemistry and Biochemistry and Department of Pharmacology
University of California, San Diego
La Jolla, California
Vincenzo Di Marzo
Istituto di Chimica Biomolecolare
Consiglio Nazionale delle Ricerche
Pozzuoli (Napoli), Italy
Wynn Esch
Mass Spectrometry Laboratory
University of Kansas
Lawrence, Kansas
Edward A. Felix
Department of Experimental Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Li Feng
Echelon Biosciences, Inc.
Salt Lake City, Utah
Colin Ferguson
Echelon Biosciences, Inc.
Salt Lake City, Utah
Jeffrey S. Forrester
The Alliance for Cellular Signaling Lipidomics Laboratory
Department of Pharmacology and the Institute for Chemical Biology
Vanderbilt University Medical Center
Nashville, Tennessee
Christopher K. Glass
Cellular and Molecular Medicine
Department of Medicine
University of California, San Diego
La Jolla, California
Richard W. Gross
Division of Bioorganic Chemistry and Molecular Pharmacology
Departments of Medicine, Molecular Biology and Pharmacology, and Chemistry
Washington University School of Medicine
St. Louis, Missouri
Xianlin Han, Ph.D.
Division of Bioorganic Chemistry and Molecular Pharmacology
Department of Medicine
Washington University School of Medicine
St. Louis, Missouri
Yusuf A. Hannun
Department of Biochemistry and Molecular Biology
Medical University of South Carolina
Charleston, South Carolina
Richard Harkewicz
University of California, San Diego
Department of Chemistry and Biochemistry and Department of Pharmacology
La Jolla, California
Yutaka Hasegawa
Department of Molecular Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Pavlina T. Ivanova
The Alliance for Cellular Signaling Lipidomics Laboratory
Department of Pharmacology and the Institute for Chemical Biology
Vanderbilt University Medical Center
Nashville, Tennessee
Jessica Krank
Department of Pharmacology
University of Colorado Health Sciences Center
Aurora, Colorado
John Lahad
Department of Molecular Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Rose Lapis
Texas Children’s Hospital–Texas Children’s Pediatric Associates
Baylor College of Medicine
Houston, Texas
Steven LeVine
Department of Molecular and Integrative Physiology
University Kansas Medical Center
Kansas City, Kansas
Alfred H. Merrill, Jr.
Georgia Institute of Technology
School of Biology
Atlanta, Georgia
Gordon B. Mills
Department of Molecular Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Stephen B. Milne
The Alliance for Cellular Signaling Lipidomics Laboratory
Department of Pharmacology and the Institute for Chemical Biology
Vanderbilt University Medical Center
Nashville, Tennessee
Andrew Morris
Department of Cell and Developmental Biology
University of North Carolina
Chapel Hill, North Carolina
Robert C. Murphy
University of Colorado Health Sciences Center
Department of Pharmacology
Aurora, Colorado
Paul O. Neilsen
Echelon Biosciences, Inc.
Salt Lake City, Utah
Robert A. Newman
Department of Experimental Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Christian Pasquali
Serono Pharmaceutical Research Institute
Serono International S.A.
Geneva, Switzerland
Glenn D. Prestwich
Department of Medicinal Chemistry
The University of Utah
Salt Lake City, Utah
Christian R.H. Raetz
Duke University Medical Center
Department of Biochemistry
Durham, North Carolina
Christian Rommel
Serono Pharmaceutical Research Institute
Serono International S.A.
Geneva, Switzerland
David W. Russell
The University of Texas
Southwestern Medical Center at Dallas
Department of Molecular Genetics
Dallas, Texas
Piotr W. Rzepecki
Echelon Biosciences, Inc.
Salt Lake City, Utah
Jyoti Shah
Division of Biology
Kansas State University
Manhattan, Kansas
Walter Shaw
Avanti Polar Lipids, Inc.
Alabaster, Alabama
Shankar Subramaniam
Department of Bioengineering
University of California, San Diego
La Jolla, California
M. Cameron Sullards, Ph.D.
Georgia Institute of Technology
School of Chemistry and Biochemistry and School of Biology
Atlanta, Georgia
Makiko Umezu-Goto
Department of Molecular Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Mario van der Stelt
NZ Organon
The Netherlands
Michael S. Van Nieuwenhze
Department of Chemistry and Biochemistry
University of California, San Diego
La Jolla, California
Xuemin Wang
Department of Biology
University of Missouri
St. Louis, Missouri
Ruth Welti
Division of Biology
Kansas State University
Manhattan, Kansas
Markus R. Wenk
Department of Biochemistry and Department of Biological Sciences
National University of Singapore
Singapore
Stephen H. White
Department of Physiology and Biophysics
University of California at Irvine
Irvine, California
Todd Williams
Mass Spectrometry Laboratory
University of Kansas
Lawrence, Kansas
Joseph L. Witztum
Department of Medicine
University of California, San Diego
La Jolla, California
Judith Wolf
Department of Gynecologic Oncology
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
John Wooley
University of California, San Diego
La Jolla, California
Yi Jin Xiao
Department of Cancer Biology
Cleveland Clinic Foundation
Cleveland, Ohio
Yan Xu
Department of Cancer Biology
Cleveland Clinic Foundation
Cleveland, Ohio
Shuangxing Yu
Department of Molecular Therapeutics
The University of Texas M.D. Anderson Cancer Center
Houston, Texas
Table of Contents
Chapter 1 The LIPID MAPS Approach to Lipidomics .......................................1
Edward A. Dennis, H. Alex Brown, Raymond A. Deems, Christopher K. Glass,
Alfred H. Merrill, Jr., Robert C. Murphy, Christian R.H. Raetz, Walter Shaw,
Shankar Subramaniam, David W. Russell, Michael S. VanNieuwenhze,
Stephen H. White, Joseph L. Witztum, and John Wooley
Chapter 2 LC/MS Methodology in Lipid Analysis and Structural
Characterization of Novel Lipid Species...........................................17
Robert C. Murphy, Jessica Krank, and Robert M. Barkley
Chapter 3 Functional Plasticity of Lipid Mediators: The Example of
Endocannabinoids ..............................................................................57
Luciano De Petrocellis, Mario van der Stelt, and Vincenzo Di Marzo
Chapter 4 Eicosanoid Lipidomics.......................................................................79
Rebecca C. Bowers-Gentry, Raymond A. Deems, Richard Harkewicz,
and Edward A. Dennis
Chapter 5 Functional Lipidomics: Lysophosphatidic Acid as a Target for
Molecular Diagnosis and Therapy of Ovarian Cancer....................101
Janos L. Tanyi, David Crotzer, Judith Wolf, Shuangxing Yu, Yutaka Hasegawa,
John Lahad, Kwai Wa Cheng, Makiko Umezu-Goto, Glenn D. Prestwich,
Andrew Morris, Robert A. Newman, Edward A. Felix, Rose Lapis, and
Gordon B. Mills
Chapter 6 Analysis of Lysophospholipids in Human Body Fluids: Comparison
of the Lysophospholipid Content in Malignant vs. Nonmalignant
Diseases ............................................................................................125
Yi Jin Xiao and Yan Xu
Chapter 7 Functional Lipidomics: Lessons and Examples from the
Sphingolipids....................................................................................147
Yusuf A. Hannun
Chapter 8 Liquid Chromatography-Tandem Mass Spectrometry
(LC-MS/MS) Analysis of Sphingolipids .........................................159
M. Cameron Sullards and Alfred H. Merrill, Jr.
Chapter 9 Methods of Probing Phosphoinositides–Protein Interactions .........189
Li Feng, Colin Ferguson, Paul O. Neilsen, Leena Chakravarty, Piotr W. Rzepecki,
and Glenn D. Prestwich
Chapter 10 Fishing for Pharmaceutically Relevant phosphoinositide-Binding
Proteins
Using Chemical Proteomics.............................................................211
Christian Pasquali and Christian Rommel
Chapter 11 Phosphoinositide Profiling in Complex Lipid Mixtures .................243
Markus R. Wenk and Pietro De Camilli
Chapter 12 Multiplexed Lipid Arrays of Antiimmunoglobulin M–Induced
Changes in the Glycerophospholipid Composition of
WEHI-231 Cells .............................................................................263
Stephen B. Milne, Jeffrey S. Forrester, Pavlina T. Ivanova, Michelle D. Armstrong,
and H. Alex Brown
Chapter 13 Specific Lipid Alterations in Alzheimer’s Disease and Diabetes:
Shotgun Global Cellular Lipidome Analyses by Electrospray
Ionization Mass Spectrometry Using Intrasource Separation.........285
Xianlin Han and Richard W. Gross
Chapter 14 High-Throughput Lipid Profiling to Identify and Characterize
Genes Involved in Lipid Metabolism, Signaling, and Stress
Response...........................................................................................307
Ruth Welti, Jyoti Shah, Steven LeVine, Wynn Esch, Todd Williams, and Xuemin Wang
Index......................................................................................................................323
