LIPIDMAPS LIPIDMAPS
OVERALL GOAL OF THE LIPID MAPS PROJECT
• Discover all major and minor lipid molecules that play a role in the biology of exemplar mammalian cells
• Construct networks of lipid maps that play a role in cellular metabolism and signaling
• Create a comprehensive resource for lipids with functional annotation of the roles they play in cellular metabolism and signaling
LIPIDMAPS LIPIDMAPS
LABORATORY DIRECTORS
• Dennis, PI and Director of Eicosanoid Core• Russel, co-PI and Director of Sterol Core• Brown, co-PI and Director of Phospholipid Core• Merrill, co-PI and Director of Sphingolipid Core• Raetz, co-PI and Director of Novel Lipids Core• Glass, co-PI and Director of Cell Biology and
Genomics Cores• Boger, co-PI and Director of Synthesis Core• Subramaniam, co-PI and Director of Bioinformatics
Core• Other co-PIs
LIPIDMAPS LIPIDMAPS
SPECIFIC GOALS OF LIPIDMAPS
• Definition of Our Systems– Cells of interest– Major and minor lipid molecules– Gene products of interest to lipid molecules
LIPIDMAPS LIPIDMAPS
CHOICE OF MACROPHAGES FOR LMAPS
-Displays important lipid biology-Likely interactions between lipids and gene products -Mammalian cell -Cell lines and murine and human cells available
-Post-mitotic-Measurable responses to lipid molecule input -Complete gene parts list likely available-Requisite mass and homogeneity -Ability to add and subtract genes -Known role of lipids in metabolism and signaling -Quantifiable phenotypes -Of interest to several diseases -Access to diseased and normal counterpart -Available to entire community
LIPIDMAPS LIPIDMAPS
Who are the players?
• Prepare an initial list of lipid players of interest
• Determine which major lipids are present in defined macrophage preparations (mass spectrometry, other)
• Quantify lipids of interest (??)• Identify genes and gene products associated
with the defined lipids (genomics, proteomics, bioinformatics, other)
LIPIDMAPS LIPIDMAPS
Players
• Major and Minor Lipids present under normal, perturbed and pathophysiological conditions.
• Identification of novel lipids through MS, lipid synthesis and characterization.
• Creation of the Lipids Database
LIPIDMAPS LIPIDMAPS
HOPANOIDS
I SOPRENOIDS
LIPID PEROXIDES
LIPOAMINO ACIDS
LIPOPOLYSACCHARIDES
LIPOPROTEINS
MYCOLIC ACIDS
PHOSPHOLIPIDS
GLYCEROPHOSPHOLIPID
PAF
SPHINGOPHOSPHOLIPID
STEROIDS
WAXES
ACYLGLYCEROLS
BILE ACIDS (CHOLANOIDS)
DERIVED LIPIDS
FATTY ACID
LONG CHAIN ALCOHOL
LONG CHAIN ALDEHYDE
LONG CHAIN BASE and CERAMIDE
EICOSANOIDS
ETHER TYPE LIPIDS
FAT SOLUBLE VITAMINS
CAROTENOID
COENZYME Q
VITAMI N A
VITAMIN D
VITAMIN E
VITAMIN K
GLYCOLIPIDS
glycoSPHINGOLIPID
glycoGLYCEROLIPID and OTHERS
LIPIDMAPS LIPIDMAPS
Gene Products• Genes that code for gene products
associated with lipid synthesis. • Regulatory elements that are
associated with expression of genes identified above.
• Proteins associated with lipid metabolism and signaling.
• Modifications of proteins involved in lipid cell biology
LIPIDMAPS LIPIDMAPS
SPECIFIC GOALS OF THE LIPIDMAPS
• Quantitate responses to stimuli– Gene expression– Mass spec identification of lipids– Protein screens– Bioinformatics
LIPIDMAPS LIPIDMAPS
Quantitate responses to stimuli
• Basal levels
• Selected stimuli affects (LPS & Others)
• Changes in gene expression
• Changes in protein concentration
• Changes in protein states
• New and novel lipids in response to stimuli
LIPIDMAPS LIPIDMAPS
Transcript Profiling
• Oligo arrays
• cDNA arrays
Design of a mouse macrophage chip
• Promoter Sequence oligo arrays
• ChIP on a chip
LIPIDMAPS LIPIDMAPS
LIPID MAPS: Bioinformatics Organizational Structure
• Shankar Subramaniam (PI)• Eoin Fahy (Coordinator) – Lipid Chemistry, MS data
analysis
• M Madhusudan – LIMS
• Dawn Cotter – LIPID MAPS Website
• Babu Guda – Lipid Biology (Genes, proteins, pathways)
• Purnima Guda – Lipid Biology (Genes, proteins, pathways)
LIPIDMAPS LIPIDMAPS
Molecular Profile ComparisonsRAW-TM-BM-ES
Chris Benner
Shankar Subramaniam & Chris Glass
UCSD Bioinformatics
LIPIDMAPS LIPIDMAPS
Macrophage Cell Types
• RAW – Macrophage cell line
• TM - Thioglycolate elicited macrophages
• BM – Bone Marrow derived macrophages
• ES – Embryonic Stem Cells (not macrophage)
LIPIDMAPS LIPIDMAPS
Abbreviation Key
• TM – Thioglycolate-induced peritoneal macrophages
• BM – Bone Marrow derived macrophages
LIPIDMAPS LIPIDMAPS
Primary Dataset
• Concentrate Efforts on Codelink data from 3 Macrophage Cell types (BM, TM, RAW)
LIPIDMAPS LIPIDMAPS
NOTX LPS LPS+DEX
Bone Marrow M0 3 3 -
Thio M0 6 6 1
Fetal Liver M0 - - -
RAW 4 4 3
Embryonic Stem 3 - -
NOTX LPS LPS+DEX
Bone Marrow M0 6 4 -
Thio M0 9 7 3
Fetal Liver M0 4 2 1
RAW - - -
Embryonic Stem - - -
CodeLink Arrays
Affymetrix Arrays
Plus multiple other conditions and KO’s…
LIPIDMAPS LIPIDMAPS
Microarray Platforms
Agilent Mouse Oligo Array
• 16,282 Probes
• 12,011 Unique LL
Codelink Mouse 10K
• 10,501 Probes
• 9,768 Unique LL• http://www.amershambiosciences.com
3672 8338 1430
