Our perception of the lipidome after the first decade of ... - Lipid Maps

PERCEPTION OF THE LIPIDOME AFTER THE
FIRST DECADE OF LIPIDOMICS
A. The LIPID MAPS Initiative
B. Example: Macrophage Eicosanoids
D. Human Plasma Lipidome and Biomarkers
Edward A. Dennis
Departments of Chemistry/Biochemistry and Pharmacology
School of Medicine, University of California, San Diego
LIPID MAPS “Glue Grant” NIH U54 GM 69338

4 base side chains
20 amino acid side chains
Lipidomics Joins
the Omics Evolution
(2009), Dennis,
PNAS, 106, 2089.
nucleic acids, amino acids,
sugars and fats: >10 5
all the fats: >10 5

Increase in Omics Citations 1985-2009
Number of Citations
Wenk MR (2010) Lipidomics:
New Tools and Applications.
Cell, 143, 888-895.
Year

Lipidomics Publications 2002-2013
Lipidomics publications
LIPID MAPS publications
Publications
Publications
Year
Year

_____________ _______________
LIPID MAPS
TM
TM
Saccharolipids / Polyketides

“CLASS”: Comprehensive
Lipidomics Analysis using
Separation Simplification
a “divide-and-conquer” strategy
category specific
(deuterated, odd-chain carbon)
category optimized
(liq-liq, SPE)
cells
tissues
sonicate
homogenate
cells or tissues
probe
internal standards
extraction
extract
medium
category specific
(GC, NP-HPLC, RP-HPLC, chiral, specialty)
GC
LC
Harkewicz & Dennis, “Applications of mass
spectrometry to lipids and membranes”
Ann Rev Biochem, 80: 301-325 (2011)
mass spectrometer
(variables)
1. Mass spectrometer types
2. Ionization mode
3. Additives (for ionization)
4. Mass spectrometer monitoring modes

Kdo 2 -Lipid A (KLA, LPS subspecies)
A specific agonist of TLR-4 on RAW 264.7 macrophages
Raetz et al., 2006, J. Lipid Res. 47: 1097
Nuclei – DAPI
Mitochondria – MitoTracker Red
O-Specific
chain
Polysaccharide
Core
Kdo
Lipid A
Glycophospholipid

Dennis et al (2010)
J. Biol. Chem, 51, 39976-85

Cellular Eicosanoid Metabolism
Buczynski, Dumlao, Dennis (2009) JLR, 50, 1015-38

COX
Cellular eicosanoid metabolism
CYP(ω)
5-LOX
CYP(EET)
Buczynski, Dumlao, Dennis, 2009, JLR, 50: 1015-38
12-LOX
15-LOX

COX
Cellular eicosanoid metabolism

Directed Proteomics on Enzymes of
Eicosanoid Biosynthesis
2
8)(#
8)($
1,6/-
7!1)
+,&0
3',)
+3$*,)&#)(41(
!),)5$#1!
+),-.)"*
)3$(#
)6$(
)+$(
)1*62
*)(00
)3$($
)3$(0
!"!#$$%"&'()*'
+),-.)"
)3$(5
)8$(
-'."#
-'."$
-'."5
)1*($
)1*(#
))-(+
))-(-
))-(*
,;32
1-$(
+)3)#
+)3)$
'!1($
1,-2
**1#
)1*+2
)1*+$
!1'02
**1% 9*215
'!1(#
-$(21#
!10(#
'&(#
'-.45
!10($
!/,-0
)1*32
)*32$
13&)
!."%
)*,#
)*,$
-!%-)
/0#1+$%"&'()*'
+),-.)"
-CDEFGHIJGE
-EGH
!"#$&
!."#$
!."35
!"#$3
-,(
670#1+$%"&'()*'
+),-.)"
!"#$!
!"#%&
')$5:
)-$*%
)-$*-
)-$*"
'&(#
)*+,
')#&#
')$%0
=>638:
')$5
')$@%
')0--
')085
')$54
')0-3
6/0#1+$%"&'()*'
+),-.)"
')083
')$%%
&

Eicosanoid Genes to Proteins to Metabolites
Proteins
Quehenberger & Dennis, New Eng. J. Medicine, 365, 1812-23 (2011)

The Beneficial Lipids in Fish Oil
• Fish oil is composed primarily of two ω-­‐3 PUFAs:
ω-­‐3
ω
Eicosapentaenoic Acid (EPA)
(C20:5, ω-­‐3)
ω-­‐3
Docosahexaenoic Acid (DHA)
(C22:6, ω-­‐3)
• Humans synthesize from essen=al fa>y acid α-­‐linolenic acid (C18:3, ω-­‐3)
ω
• EPA is found at barely detectable levels in humans
• DHA is more abundant than EPA; found primarily in the brain and re=na

Arachidonic Acid Serves as a
Precursor for Many Eicosanoids
EPA/DHA
Are eicosanoids less pro-inflammatory when derived from EPA/DHA

Effects of PUFA Supplementation on ATP
Stimulated COX-1 and 5-LOX Signaling
Norris & Dennis, PNAS (2012) 109, 8517

Omega-3 Implications for Nutrition
• The global effects of EPA and DHA on normal lipid
metabolism can be quantitatively studied.
• EPA and DHA affect the overall eicosadome decreasing
production of some, but not all, AA-derived eicosanoids.
• There is a concomitant increase in specific EPA- and
DHA-derived metabolites.
• Deciphering the role of fish oil-derived ω-3 EPA and DHA
in inflammatory eicosanoid signaling provides insight as
to their role as therapeutic/nutritional agents.
Norris & Dennis, PNAS (2012) 109, 8517

NIST collected (pooled) fasting plasma from 100 individuals
50% female and 50% male; age 40-50
15% of the total taken from
individuals of Hispanic origin!

Human Plasma Metabolites (mg/dL)
Nucleic Acids
Lipids
Amino Acids
Sugars

Human Plasma Lipid Categories (µM)
Sterol Lipids
Sphingolipids
Fatty Acyls
Glycerolipids
Glycerophospholipids
Prenols

Human Plasma Lipid Diversity
J Lipid Res, 51, 3299-3305 (2010)

Plasma Lipids in the Metabolic Syndrome
Quehenberger & Dennis, New Eng. J. Medicine, 365, 1812-23 (2011)

Charles Brown
Univ. of Missouri
George Kokotos
Univ. of Athens
Kang Zhang
Varnavas Mouchlis Matt Buczynski John Burke Yasu Kihara
Tony Yaksh
Virgil Woods
Eduard Sabidó
Ruedi Aebersold
Alex Andreyev Howard Hsu Oswald Quehenberger Paul Norris
Chris Glass
Eoin Fahy
S. Subramaniam
Andy McCammon
Darren Dumlao Ann Gregus Jian Cao Aaron Armando Ishita Shah

The LIPID MAPS Consortium
L-R: C.R.H. Raetz, J.L. Witztum, N. Winograd, A.H. Merrill, R.C. Murphy, M.S. VanNieuwenhze,
E.A. Dennis, D.W. Russell, W.A. Shaw, C.K. Glass, J. Chin (NIH), S. Subramaniam, H.A. Brown