Analysis of Lipid Metabolites. = Lipidomics

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1 Analysis of Lipid Metabolites = Lipidomics Pentti Somerharju Transmed

2 utline of the talk What is Lipidomics? Where is lipidomics needed? Lipid classes and their functions Why mass-spectrometric analysis? Targeted or nontargeted analysis? ow to improve selectivity of detection? Data analysis and interpretation Dynamic lipidomics (study on lipid metabolism) Glycerophospholipid homeostasis Regulation of synthesis Regulation of degradation Coordination by superlattice formation?

3 Lipidome is part of the metabolome DIET Functional Lipidomics = ow other molecules affect the lipidome and vice versa

4 Where is lipidomics needed? Biology Functions of lipids? Regulation lipid composition of membranes? Clinics Search of diagnostic/predictive markers Search of drugs targeting lipid disorders Industry Modification of fats and oils Quality control

5 Significance of lipidomic data? Very similar changes in lipidome when P53 or ApoE is knocked out =>Changes in lipidome can be nonspecific! False biomarkers also when the number of lipids analyzed exceeds the number of samples (patients) Many confounding factors: diet, gut microbiota, physical activity, age, genetic background etc

6 Targeted analysis When you know what you are looking for (e.g. studies on lipid homeostasis) Selective detection (MS/MS or LC-SRM) Nontargeted analysis When you do not know (search for disease markers/biomarkers) Nonselective detection (LC-MS)

7 Mammalian Lipid classes and their main Functions

8 Glycerophospholipids 2 C C C 2 P N >10 classes (PC, PE, PS, PI, PA etc) Each class consists of numerous species due to different fatty acid combinations => Thousands of different species possible! Functions: Main structural components of membranes Second messengers in signal transduction Regulators of membrane trafficking etc Phosphatidylcholine

9 Apolar (neutral) lipids C 2 C C 2 Fatty acids Structural componets of other lipids Energy source/storage Precursors of eicosanoids etc Acylglycerols (TG etc) Fatty acid storage and transport undreads of species possible Cholesteryl esters Storage forms of cholesterol

10 Glygosphingolipids C 2 C C C N Tens of different classes (head groups) Many different fatty acid => undreads of possible species Functions Structural component of membranes Cell-cell regognition Signal transduction Lactosylceramide

11 ther lipid classes Sterols (cholesterol etc) Structural components of membranes Precursor or steroid hormones Eicosanoids (prostagandins etc) Signaling Prenol lipids Membrane anchors in some proteins

12 A mammalian cell may contain thousands of differerent lipid species! The biological challenge: Why? Each lipid species has a specific function? No..most lipids act in an ensemble!

13 The Analytical challenge ow to quantify so many species with so different properties and present at so different concentrations?...with Mass Spectrometry!

14 Advantages of mass-spectrometry Conventional analysis (PL) 1. Lipid extraction 2. Separation of lipid classes by TLC or PLC 3. Separation of molecular species by PLC 4. Treatment by phospholipase A2 5. Analysis of fatty acids by GC 6. Data processing Slow (several days) Low sensitivity Plenty of manual work MS-analysis 1. Lipid extraction 2. MS/MS or LC-MS analysis 3. Data processing Fast (even less than 1 hour) Very high sensitivity Can be automated

15 Which ionization mode? Electrospray (ESI) Does not cause fragmentation Compatible with on-line LC Matrix-assisted laser desorption (MALDI) Used less due to e.g. suppression effects => All lipids not detected

16 Electrospray ionization Competition for charge => Suppression effects!

17 Which mass analyser? Triple quadrupole Workhorse of lipidomics Allows precursor and neutral-loss scanning = Lipid class-specific detection Modestly (?) priced Fourier transform or rbitrap Very high mass resolution and accuracy Allow detailed analysis of lipid structure Very expensive!

18 Direct MS scanning (triple quadrupole) Scanning MS1 Collision cell MS2 Detector MS- spectrum of ela cell lipid extract ela in C/M/2P 1:2: mM N4Ac 100 % > More resolution/selectivity needed! PIs

19 Means to improve resolution MS/MS (tandem MS) LC-MS (with SRM)

20 Lipid class -specific scanning Phospholipid class consist of species with the same polar head-group but different fatty acid combination C 2 C 2 C P X Phospholipid class Specific scan Phosphatidylcholines Precursors of +184 Phosphatidylinositols Precursors of -241 Phosphatidylethanolamines Neutral-loss of 141 Phosphatidylserines Neutral-loss of 87

21 Precursor ion scanning Requires a characteristic, charged product ion PC => Diglyceride + phosphocholine (+184) Scanning Fragmentation Static (+184) Quadrupole 1 mass filter Collision cell (elium or Argon) Quadrupole 2 mass filter

22 Precursors of +184 => PC + SM SM-16:0 -Alkaline hydrolysis can be used to remove PCs

23 Neutral-loss scanning..when the characteristic fragment is uncharged PE => Diglyceride (+) + phosphoethanolamine (141) Mass interval = 141 Scanning Fragmentation Scanning Qaudrupole 1 Collision cell Quadrupole 2

24 Selective detection of PE, PS and PI ela-cells +CTRL-siRNA + D9Chol+D4-EA+D3-Ser +A Allstar 4h 9 1 (2.514) Sb (1,40.00 ); Sm (SG, 10x0.50); Sm (SG, 10x0.50) Neutral Loss 141ES e5 % PE Allstar 4h 3 1 (3.019) Sb (1,40.00 ); Sm (SG, 10x0.50) Neutral Loss 87ES e5 % ; PS Allstar 4h 5 1 (3.123) Sb (1,40.00 ); Sm (SG, 10x0.50) Parents of 241ES e5 PI Martinilta kuva MS- ja muut % m/z

25 Analysis of Sphingolipids

26 C AcN C 3 S 3 - C 2 C N C C C 2 C N C C C 2 C N C C AcN C 2 C C C N C 2 C N C C 3 S 3 - Sphingosine Ceramide Lactosylceramide Ganglioside Sulfatide

27 Ceramide and Neutral Glycosphingolipids - Precursors of sphingosine (m/z +264) Glucosylceramides Ceramides 24:1

28 Sulfatides - Precursors of sulfate (m/z -97)

29 Quantification is not simple because intensity depends on: Lipid head-group structure Acyl chain length Acyl chain unsaturation Ions present (adduct formation) Detergent and other impurities (suppression) Solvent composition and instrument settings => Internal standards necessary!

30 Data analysis software is essential LIMSA LIMSA does: Peak picking and fitting Peak overlap correction Peak assignment (database of >3000 lipids) Quantification using internal standards

31 PAUSE

32 Dynamic Lipidomics: Analysis of lipid Metabolism Biosynthesis Degradation Precursors: Choline, ethanolamine, glycerol, fatty acids, Sphingosine, monosaccharides etc 2 or 13 C -labeled

33 Selective detection of headgroup-labeled PCs D 9 -PC > Diglyceride + D 9 -Phosphocholine (+193) PI +184 PI +193 Intensity m /z

34 LC-MS/MS with selective reaction monitoring 100 TIC TIC % % => 193 (D 9 -PC) > 193 (d9-pc-34:2) 5.46 e % => 184 (PC) > 184 (PC-34:2) 9.66 e Time

35 Selective detection of other labeled GPLs D 6 -PI = Precursors of -247 D 4 -PE = Neutral loss of 145 D 3 -PS = Neutral loss of 90 Specific labeling is easy to determine All precursors can be present simultaneously!

36 ow a cell maintains the phospholipid homeostatis of its membranes? Biosynthesis Remodeling Degradation Trafficking ow are these coordinated?

37 Biosynthesis

38 Biosynthesis of Glycerophospholipids Glycerol-3-P DAP Choline 1-acyl-G-3-P 1-acyl-DAP CDP-choline CT Choline-P PA PC PSS1 PG-P CDP-DG + Inositol DAG PE PSS2 PS PG PI CDP-Ethanolamine CL Ethanolamine-P Ethanolamine

39 ur studies on GPL biosynthesis PRTCL Label cellular GPLs using a mix of D 9 -choline, D 4 -ethanolamine, D 3 -serine and D 6 -inositol Load a GPL to cells using m -CD Incubate and extract lipids Quantify the labeled and unlabeled GPLs by MS using G-specific scans

40 Introduction of GPLs to cells using Cyclodextrin Purpose: 1. Introduction of exogenous labeled GPLs to cells 2. Perturbation of GPL homeostasis => Concentration of a GPL can be encreased by % without compromizing cell viability (Kainu et al. J. Lipid Res. 2010)

41 PI loading inhibits PI synthesis 0,9 CTRL PI-vesicles lableled / unlabeled 0,6 0,3 0, Time (h)

42 PE loading inhibits PE synthesis 0,8 0,7 0,6 CTRL PE-vesicles lableled / unlabeled 0,5 0,4 0,3 0,2 0,1 0, Time (h)

43 PS loading blocks PS synthesis 1,2 CTRL PS-vesicles lableled/unlabeled 0,9 0,6 0,3 0, Time (h)

44 PC loading inhibits PC synthesis 1,2 CTRL PC-vesicles lableled / unlabeled 0,9 0,6 0,3 0, Time (h)

45 Product inhibition is specific! But the details of the mechanism remains unknown.. Reversal on biosynthesis??

46 Degradation

47 A-type phospholipases (PLAs) are important players in GPL homeostasis because: Boosting of the biosynthesis of a phospholipid class does not increase its cellular content -E.g. over-expression of cytidyl transferase in ela cells did not increase tha amount of PC significantly (Baburina & Jackowski 1999) but the concentration of the deacylation product (glycerophospholine) was greatly increased -Analogous data have been obtained for PE and PS Which PLAs are involved?

48 Protocol to identify the homeostatic PLAs 1. Determine which PLAs expressed in ela cells Ca2+-independent PLAs ipla-beta ipla-gamma ipla 2 -delta ipla 2 -epsilon ipla 2 -zeta ipla 2 -eta + several cplas and splas (not considered homeostatic) 2. Knock-down each ipla in turn using RNAi 3. Determine effects on phospholipid turnover using labeled precursors and MS-analysis 4. Purify the implicated iplas and determine specificity and regulation in vitro (and in vivo..)

49 PC turnover is 50% slower in ipla knock-down cells D9-labeled / Unlabeled PC T 1/2 = 12.5h T 1/2 = 18.7h CTRL sirna ibeta sirna Chase (h)

50 Also PE and PS turnover is decreased in ipla -knock down cells Similar results for ipla-delta and -gamma

51 pen questions: ow do the homeostatic PLAs sense the proper composition, i.e. how they are regulated? ow biosynthesis and degardation are coordinated?

52 Does ipla- activity depend on substrate efflux propensity? Burke JE, Dennis EA (2009) J. Lipid Res. 50:S237-S242

53 MS-based assay of PLA specificity => igh throughput => No matrix ambiquiety! Protocol Mix the phospholipids (>100 different allowed) Make vesicles Add a phospholipase Incubate and take samples at intervals Extract lipids and analyze by MS

54 Effects of acyl chain length and unsaturation on hydrolysis by PLA Mixture of 27 PC species: - Acyl Chain lenght = 6-22 carbons - Double bonds = 0-12 per molecule

55 100 A STD 0 min STD = Shingomyelin Relative Intesity (%) STD 3 min m/z [species]/t 0 1,00 0,75 0,50 0,25 B E G F C20 C21 C25 0, Time (min)

56 Activity of ipla- deceases with increasing substrate hydrophobicity 3,5 3,0 PC-mix ydrolysis decreases strongly with acyl chain length Relative rate of hydrolysis 2,5 2,0 1,5 1,0 0,5 0, Total acyl chain carbons ydrolysis increases with increasing unsaturation Substarate efflux is ratelimiting?

57 Efflux propensity can be determined from the rate of interbilayer translocation

58 Transfer rate (h -1 ) 10 0,1 1E-3 1E-5 A Relative hydrolysis rate 1E-7 1 0,1 B 0, Total acyl chain carbon number

59 ow could efflux regulate homeostatic PLAs in vivo? Superlattice Model predics that efflux propensity (chemical activity) increases abruptly at critical compositions

60 Superlattice model => nly a limited number of allowed compositions!

61 Two-component bilyers X guest = 1/(a 2 + a * b + b 2 )

62 Superlattices are dynamic minimum-energy structures

63 Regular distribution represent the lowest free energy state of the bilayer because it: 1. Allows optimal packing of different lipids in the bilayer 2. Minimizes the proximity of charged lipids

64 ptimimal packing of lipids with complementary shapes Suboptimal packing ptimal packing

65 Minimal charge-charge repulsion

66 Regulation of homeostatic phospholipases by Superlattice formation? Excess of lipid A => Enhanced efflux (fugality) => ydrolysis of by a homeostatic PLA

67 Regulation of biosynthetic enzymes by Superlattice formation Excess of a phospholipid A => Increased chemical activity of A => Increased feed-back inhibition of the synthetic enzyme

68 SL-based regulation of synthesis and degradation Synthesis PC Degradation Synthesis PE Degradation PC-Regulator PE- Regulator PS-Regulator PI- Regulator Synthesis PS Degradation Synthesis PI Degradation - Simple mechanism that minimises compositional fluctuations

69 Conclusions eavy-isotope labeled precursors combined with Mass spectrometry is a superior tool to study GPL metabolism Feed-back -inhibition by the end product seems to regulate the biosynthesis of major GPLs Substrate efflux propensity could regulate the activity of homeostatic PLAs Superlattice formation could coordinate synthesis and degradation by modulating the chemical activity/efflux propensity of GPLs