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Lipidomics comes of age in nutrition and othertranslational sciences A. Lipidomics and Nutrition B. Examples C. Additional perspectives Alfred H. Merrill, Jr. Schools of Biology, Biochemistry & Chemistry and the Petit Institute for Bioengineering and Biosciences Georgia Institute of Technology Omic categories: (partial list) Genomics (Epigenomics) Transcriptomics Proteomics Glycomics (posttranslational modifications) Gene mRNA miRNA Protein Protein-protein interactions Post-translational modification(s) Metabolomics Metabolites Cell functions & regulatory mechanisms Embryogenesis to aging (disease) Systems Biology Lipidomics & Nutrition: Nutrients Toxins etc. Nutrition is a fundamental component of systems biology at all levels, and especially the metabolome. Embryogenesis to aging (disease) Systems Biology Genomics (Epigenomics) Transcriptomics Proteomics Glycomics (posttranslational modifications) Gene mRNA miRNA Protein Protein-protein interactions Post-translational modification(s) Metabolomics Metabolites Cell functions & regulatory mechanisms Omic categories: (partial list) J. Nutr. 1: 191, 1928. Lipidomics & Nutrition: Nutrients Toxins etc. The field of nutrition has been concerned about the question of how many molecules are present and the amounts for a long time. Omic categories: recognize the importance Gene of (partial list) metabolomics, as indicated in this opinion piece from 2002 that Genomics is still relevant today. (Epigenomics) mRNA Transcriptomics Proteomics Glycomics (posttranslational modifications) miRNA Protein Protein-protein interactions Post-translational modification(s) Embryogenesis to aging (disease) J. Nutr. 1: 191, 1928. Cell functions & regulatory mechanisms Systems Biology …and was one of the first to Environment J. Nutr. 132: 2486–2487, 2002. Nutrients Toxins etc. Metabolomics “Metabolomics does not have the luxury of a single class of analyte nor a single mode of analysis and the field of metabolomics will Metabolites continue to be driven by technological developments.” Omic categories: (partial list) Genomics (Epigenomics) mRNA Transcriptomics Proteomics Glycomics (posttranslational modifications) Protein Protein-protein interactions Post-translational modification(s) Metabolomics Lipidomics Metabolites Cell functions & regulatory mechanisms Systems Biology Rationale for lipidomics in nutrition: Embryogenesis to aging (disease) Lipids are one of the most structurally diverse, multifunctional biomolecules, and may constitute the largest Gene “omic” category. This presents both analytical and conceptual challenges. Environment Nutrients Toxins etc. Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed Better understanding of: Digestion Absorption Transport Metabolism Factors impacting metabolism Molecular function An organism, as in the cartoon here, is basically an eating, food processing, and excretion machine. GI microbiome metabolism/metabolites Excretion Lipidomics ultimately wants to understand the correlations between consumption and health & disease. Levels where lipidomics has been/can be helpful to There are many groups already measuring large nutrition (and some other translational disciplines) numbers of compounds in food and relating their Better understanding of: consumption to health. molecular subspecies in food (& the environment) and the amounts consumed Better understanding of: Digestion Absorption Transport Metabolism Factors impacting metabolism Molecular function GI microbiome metabolism/metabolites Advantages: Easy access; well established; reliable Excretion Disadvantages: For the most part, covers only known nutrients Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed Lipidomics in nutrition and Better understanding of: food research. Hyötyläinen Digestion T, Bondia-Pons I, Orešič M. Absorption Mol Nutr Food Res. 2013 Transport Feb 15. PMID: 23413227 Metabolism Factors impacting metabolism Foodomics: a new The field of nutrition has Molecular function comprehensive approach to food and nutrition. Capozzi been concerned about the GImany microbiome metabolism/metabolites F, Bordoni A. question of how Genes Nutr. 8:1-4 (2013) molecules are present and Excretion the amounts for a long time. Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed Better understanding of: Digestion Absorption Transport Anal Chem. 85:1114-23 (2013). Metabolism Factors impacting metabolism Molecular function GI microbiome metabolism/metabolites Excretion The topic even encompasses the fecal lipidome. Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed Better understanding of: Digestion Absorption Transport Metabolism Factors impacting metabolism Molecular function GI microbiome metabolism/metabolites Excretion The field of sphingolipidomics began with the discovery of sphingosine. The sphingolipid backbone(s) Sphingoid bases “Sphingosines” (named for “…the many enigmas which it presented to the inquirer…”) 1884 1881 N-acyl-sphingoid bases (“Ceramides”) J. L. W. Thudichum Cookery. Its Art and Practice (1895) Thudichum was also very interested in food chemistry. Physiologic deduction proves that perfect cookery is the greatest economy …[for]… production of the highest physiological force… It is believed and hoped that the medical profession will find in this work many materials to assist them in dietetic disquisitions, and in the synthesis of rules to give into the hands of patients or their providers. Such advice is often asked for, and is always well received; and this experience has been one of the motives for the composition of this treatise. p. vi-vii Levels where lipidomics has been/can be helpful to Usual mammalian nutrition (and some other translational disciplines) sphingolipids. The first step is a better understanding of: molecular subspecies in food (& the environment) and the amounts consumed OH NH2 Spisulosine (1-deoxysphinganine) OH NH2 Obscuraminol HO O HO O O O O Examples of novel O compounds from O HO OHO other sources. OH OH Fumonisin B1 OH NH2 Biodiversity of sphingoid bases ("sphingosines") and related amino alcohols. ST Pruett et al., J Lipid Res. 49:1621-39 (2008). Sphingolipid and glycosphingolipid metabolic pathways in the era of sphingolipidomics. AH Merrill Jr. Chem Rev 111:6387-422 (2011). Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed OH Spisulosine (1-deoxysphinganine) ES-285 NH2 Spisula polynyma 1-deoxysphinganines were first found in other organisms. Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed OH Spisulosine (1-deoxysphinganine) ES-285 NH2 Spisula polynyma The marine compound spisulosine, an inhibitor of cell proliferation, promotes the disassembly of actin stress fibers. R. Cuadros et al., Cancer Lett. 152:23-9 (2000). Phase I dose-escalating study of ES-285 given as a three-hour intravenous infusion every three weeks in patients with advanced malignant solid tumors. C. Massard et al., Invest New Drugs. 30:2318-26 (2012). Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed OH 1-deoxysphinganine (-osine) NH2 pmol/g dry weight pmol/g dry weight Predicted site of N-acylation N-acyl-chain derivatives of 1-deoxysphinganine (1-deoxyDHCer) and 1-deoxysphingosine (1-deoxy-Cer) in beef and octopus. They are usually present as the N-acyl-derivatives, and in many foods. These data are from ongoing studies of novel 1-deoxy-sphingolipids in food OH NH 2 1-deoxysphinganine (-osine) Site of N-acylation Better understanding of: molecular subspecies in food (& the environment) and the amounts consumed Sum of the analyzed N-acyl-chain derivatives of 1-deoxysphinganine (1-deoxyDHCer) and 1-deoxysphingosine (1-deoxy-Cer) in the foods shown. From Ongoing studies of novel 1-deoxy-sphingolipids in food Sphingolipids in selected foods and yearly consumption per capita Product Sphingolipid content Consumption per capita The presence _________________________________________________________________________ of mmol/kg mmol/year (g/year) sphingolipids Modulation of intracellular betain foodDairy products 38.5 catenin localization and intestinal appears to Milk (3.5%) 0.16 5.76 tumorigenesis in vivo and in vitro Lowfat Milk (<2%) 0.09 5.49 have an Cheese (29%) 1.33 15.9 by sphingolipids. impact on Frozen dairy (11%) 0.50 7.04 EM Schmelz et al., Cancer Res cancer. Butter 0.46 0.92 61:6723-9 (2001) Eggs 2.25 14 Total meat products Beef & veal Chicken & turkey Fish0.50 Vegetables Potato Tomato Soybeans Fruits and nuts Cereals 0.39 0.39 to 0.53 0.13 0.04 to 2.4 0.69 0.42 2.4 0.07 to 0.8 0.58 34.3 11.3 14.0 0.9 8.1 to 34 4.1 1.7 n.a. 3.2 38 Suppression of breast xenograft growth and progression in nude mice: implications for the use of orally administered sphingolipids as chemopreventive agents against breast cancer. KW Simon et al., Food Funct. 1:90-8 (2010). Total per year: 153 to 181 116 to 139 _________________________________________________________________________ Vesper et al., J. Nutr.129: 1239-1250 (1999). HO What is (are) factors that might limit the effectiveness of dietary sphingolipids (i.e., the sphingoid bases after digestion) as anti-cancer agents? HO Absorption of sphingoid bases from complex sphingolipids NH3(+) R HO HO NH3(+) HO NH2 HO R R R R HO NH3(+) HO HO HO The “usual” types of sphingoid bases are mainly degraded in the intestinal cells. Intracellular targets: (-) cancer (+) cancer HO NH2 Sphingosine kinase R Degraded to fatty aldehyde + NH3(+) ethanolamine-P O PO3= Blood Intestinal lumen HO HO HO NH3(+) R versus: Absorption of sphingoid bases w/o hydroxyl at carbon 1 HO NH2 HO HO NH3(+) HO HO HO NH2 R HO NH2 NH3(+) NH2 R HO NH3(+) HO R R R HO NH3(+) NH2 R R HO R HO R R Absorption of sphingoid bases from complex sphingolipids NH3(+) R Bound to albumin and RBC NH3(+) Intracellular targets: (-) cancer (+) cancer R R HO NH3(+) HO HO Sphingosine kinase R HO O PO3= NH3(+) HO NH2 Degraded to fatty aldehyde + ethanolamine-P 1-deoxysphingoid bases are more likely to be Blood absorbed. Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food & Metabolism Factors impacting metabolism Where did we first note 1Molecular function deooxysphingoid bases in mammals? OH N-acyl-metabolites NH2 Spisulosine (1-deoxysphinganine) HO O HO O O O OH O HO O O OHO OH Fumonisin B1 OH NH2 Ceramide synthase Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food & Metabolism Factors impacting metabolism Molecular function OH N-acyl-metabolites Spisulosine (1-deoxysphinganine) NH2 Ceramide synthase Origin of 1-deoxy-sphingoid bases? Utilization of both Ser and Ala by serine palmitoyltranserease, the first enzyme of sphingolipid biosynthesis. While wild type SPT utilizes Ser>Ala, Hornemann et al. (2009) have found that SPT muations in human sensory neuropathies (HSN) result in elevated Ala utilization and biosynthesis of 1-deoxy-sphingolipids, which appear to be major contributors to the neuropathology. Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Better understanding of: molecular subspecies in food & Metabolism Factors impacting metabolism Molecular function Glycolysis, TCA cycle, transaminations Pyruvate One carbon pool Glycine Serine Alanine Serine palmitoyltransferase Sphinganine OH OH R NH2 OH R 1-(Desoxymethyl)sphinganine OH R NH2 1-Deoxysphinganine NH2 N-acylation (1-deoxy…)-dihydroceramides then desaturation (1-deoxy…)-ceramides Thus, the factors that govern the amounts of 1-deoxy- sphingolipids that are made are de novo: a) Precursor availability b) SPT wild type and/or mutations Different sphingoid bases are made when the precursor supply is modulated, or when SPT is mutated. Levels where lipidomics has been/can be helpful to nutrition (and some other translational disciplines) Implications? Can also be neurotoxic Glycolysis, TCA cycle, transaminations Pyruvate One carbon pool Glycine Serine Alanine Serine palmitoyltransferase Sphinganine OH J Clin Invest. 121:4735–4745 (2011) OH R NH2 OH R 1-(Desoxymethyl)sphinganine OH R NH2 1-Deoxysphinganine NH2 N-acylation (1-deoxy…)-dihydroceramides then desaturation (1-deoxy…)-ceramides Endogenous vs exogenous 1-deoxysphingoid bases? Up to this point, we have discussed only a few of the simple backbone variants, whereas, the major species in mammals are N-acyl-metabolites and beyond, with >500 headgroup elaborations (download available at www.sphingomap.org) 26 SPT Serine + Palmitoyl-CoA Reductase 3-Ketosphinganine (3-Keto-m18:0) Sphinganine (d18:0) SMS d18:0 c18:0 DHCerP d18:0 c20:0 DHSM d18:0 c22:0 DHSM d18:0 c20:0 DHCerP d18:0 c22:0 DHCerP d18:0 c24:1 DHSM d18:0 c24:1 DHCerP d18:0 c24:0 DHSM d18:0 c24:0 DHCerP d18:0 c26:1 DHSM d18:0 c26:1 DHCerP d18:0 c26:0 DHSM d18:0 c26:0 DHCerP d18:0 c18:0 GlcDH d18:0; c20:0 DHCer d18:0 c18:0 GalDH SM GalCer synthase d18:1 c18:0 Glc d18:1 c16:0 Gal Sulfate------ Gal (ST) d18:1 c16:0 Galβ1------- 4Glc (LacCer) d18:1 c16:0 d18:0 c20:0 GalDH SM CerP d18:0 c22:0 GlcDH d18:0 c22:0 GalDH d18:0; c24:1 DHCer d18:0 c24:1 GlcDH d18:0 c24:1 GalDH d18:0; c24:0 DHCer d18:0 c24:0 GlcDH d18:0 c24:0 GalDH d18:0; c26:1 DHCer d18:0 c26:1 GlcDH d18:0 c26:1 GalDH d18:0; c26:0 DHCer d18:0 c26:0 GlcDH SM CerP SM CerP SM CerP SM CerP d18:0 c26:0 GalDH SM CerP 3 unique samples (ranging to 100 µL)d18:1; d18:0; d18:1; d18:1; from 1 d18:1; c20:0 c22:0 c24:1 c24:0 c26:1 and sample preps Cer Cer Cer Cer Cer 6 unique LC-MS/MS analyses CERK d18:1; c16:0 Cer d18:0 c20:0 GlcDH d18:0; c22:0 DHCer Dihydroceramide desaturases Analysis of more complex mammalian sphingolipids by LC-MS/MS d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 d18:1 (from 3-ketosphinganine simple & sulfatides): c18:0 c20:0 c22:0 c24:1 c24:0 gangliosides c26:1 c26:0 c18:0 c20:0 c22:0 through c24:1 c24:0 c26:1 c26:0 d18:1 c16:0 CerP SMS d18:0; c18:0 DHCer GalCer synthase d18:0 c16:0 GalDH d18:1 c16:0 SM d18:1 c16:0 Glc d18:0 c18:0 DHSM CerS3 (> c24) CERK d18:0; c16:0 DHCer d18:0 c16:0 GlcDH GlcCer synthase Sphingosine (d18:1) Ceramidases GlcCer synthase Sphingosine 1-P (d18:0-P) CerS2 (c22,24) CerS4 (c20 + 2) CerS1 (c18) d18:0 c16:0 DHCerP SphK NH2 Hexadec(an/en)al + Ethanolamine-P Lyase SphK CerS5 (c16) & 6 (c14 & 16) d18:0 c16:0 DHSM Sphinganine 1-P (d18:0-P) OH OH d18:0; c18:0 Cer d18:1 c20:0 Glc d18:1 c18:0 Gal d18:1 c22:0 Glc d18:1 c20:0 Gal d18:1 c22:0 Gal d18:1 c24:1 Glc d18:1 c24:1 Gal d18:1 c24:0 Glc d18:1 c24:0 Gal d18:1 c26:1 Glc d18:1 c26:1 Gal CerP d18:1; c26:0 Cer d18:1 c26:0 Glc plus tissue slices for tissue imaging mass spectrometry. Sulfate------ Gal (ST) d18:1 c18:0 Galβ1------- 4Glc (LacCer) d18:1 c18:0 Sulfate------ Gal (ST) d18:1 c20:0 Sulfate------ Gal (ST) d18:1 c22:0 Sulfate------ Gal (ST) d18:1 c24:1 Sulfate------ Gal (ST) d18:1 c24:0 Sulfate------ Gal (ST) d18:1 c26:1 d18:1 c26:0 Gal Sulfate------ Gal (ST) d18:1 c26:0 MC Sullards et al., Biochim Biophys Acta 1811:838-53 (2011) Galβ1------- 4Glc (LacCer) d18:1 c20:0 Galβ1------- 4Glc (LacCer) d18:1 c22:0 Galβ1------- 4Glc (LacCer) d18:1 c24:1 Galβ1------- 4Glc (LacCer) d18:1 c24:0 Galβ1------- 4Glc (LacCer) d18:1 c26:1 Galβ1------- 4Glc (LacCer) d18:1 c26:0 Single phase extraction (w/internal standards) Biological sample Analytes Column/MS Sphingoid bases S1P, Sa1P Cer1P Sulfatides Reverse phase column (C18) QQQ or Qtrap Gangliosides Organic phase Extraction (w/internal standards) Ionization mode + + - OrbiTrap Cer, HexCer, Normal phase LacCer, SM, column (LC-NH2) (Cer1P, QQQ or QTrap Sulfatides) Normal phase GlcCer, column (LC-Si) GalCer QQQ or QTrap Normalization aliquot (DNA, Protein, Cell #, etc) + + For complex glycoSL we are using the Thermo LTQ Orbitrap XL & Eksigent NanoLC 2D a) Hybrid Linear Ion trap / Orbitrap – 2 instruments that can be operated in series or parallel b) Orbi – 10-100K resolution, < 3ppm mass accuracy c) LTQ XL - MS1-10 for molecular connectivity relationships d) CID, PQD, HCD, ETD e) 2D Liquid Chromatography SAX / RP Merrill, A. H., Jr. Chem. Rev. 111, 6387-6422 (2011) Relative Abundance GM1 – h38:1, -1.2 ppm 1588.8926 100 90 1589.8951 80 NL: 7.45E4 mcs0030_120411133232 #1499-1516 RT: 36.42-36.83 AV: 18 T: FTMS - p ESI Full ms [500.00-2000.00] 70 60 50 1590.8989 40 30 20 10 1591.8997 0 NL: 4.02E5 1588.8945 100 C 75 H 134 N 3 O 32 : C 75 H 134 N 3 O 32 pa Chrg 1 90 1589.8978 80 70 60 50 40 Example spectra 1590.9012 30 20 1591.9046 10 0 1587 1588 1589 1590 1591 m/z 1592 1593 1594 NL: 1.22E5 mcs0030_120411133232 #1483-1500 RT: 36.03-36.45 AV: 18 T: FTMS - p ESI Full ms [500.00-2000.00] 925.4747 100 80 60 933.4721 926.4780 40 934.4753 926.9793 20 Relative Abundance 0 100 934.9769 931.5184 927.4810 NL: 3.56E5 925.4751 925.9768 80 C 84 H 146 N 4 O 40 : C 84 H 146 N 4 O 40 pa Chrg 2 GD1 – h35:1, -0.4ppm 60 926.4785 40 20 926.9802 0 100 NL: 3.55E5 933.4726 933.9743 C 84 H 146 N 4 O 41 : C 84 H 146 N 4 O 41 pa Chrg 2 GD1 – 2h35:1, -0.5ppm 80 60 934.4759 40 20 934.9776 0 923 924 925 926 927 928 929 930 m/z 931 932 933 934 935 936 Relative Abundance NL: 8.59E4 mcs0030_120411133232 #1503-1521 RT: 36.52-36.96 AV: 19 T: FTMS - p ESI Full ms [500.00-2000.00] GT1 – h36:2, -0.7ppm 1070.5161 100 90 1070.0142 80 70 1071.0175 60 50 40 1071.5195 30 20 1072.0215 10 0 100 1070.0150 NL: 3.17E5 1070.5167 C 95 H 161 N 5 O 48 : C 95 H 161 N 5 O 48 pa Chrg 2 90 80 70 60 1071.0184 50 40 30 20 1071.5200 10 1072.0205 0 1068.5 1069.0 1069.5 1070.0 1070.5 1071.0 m/z 1071.5 1072.0 1072.5 1073.0 1073.5 mcs0031_120412122915 4/12/2012 12:29:15 PM Add liquid chromatography GM2 RT: 49.93 - 55.03 100 Relative Abundance 90 52.42 52.95 GM1 80 GM3 53.22 53.05 70 NL: 1.13E6 m/z= 1207.71961207.8007 MS mcs0031_12041212 2915 NL: 2.34E6 m/z= 1410.79881410.8953 MS mcs0031_12041212 2915 NL: 3.36E6 m/z= 1572.83121572.9470 MS mcs0031_12041212 2915 53.32 60 50 40 30 20 10 0 50.0 50.5 51.0 mcs0031_120412122915 #2145-2202 RT: 52.13-53.51 T: FTMS - p ESI Full ms [500.00-2000.00] 51.5 52.0 52.5 Time (min) 53.0 53.5 54.5 55.0 AV: 58 NL: 6.82E5 1572.8950 100 Relative Abundance 54.0 90 80 70 1410.8434 60 808.9471 50 40 1207.7650 30 20 10 727.9207 1382.8129 0 600 700 800 900 1000 1100 1200 1300 m/z 1400 1500 1600 1700 1800 1900 2000 RT: 36.83 - 64.80 NL: 3.41E7 TIC MS mcs0031_1 2041212291 5 48.36 100 GM1 95 90 85 36:1 80 47.94 75 Relative Abundance 70 65 38:1 60 55 37:1 50 45 52.42 40 h36:0 35 36:0 30 34:1 25 40:1 38:0 36:2 52.95 20 53.05 44.10 15 53.20 50.38 10 5 58.30 54.65 45.10 45.15 43.28 55.24 55.31 57.06 58.84 57.13 58.91 60.59 60.66 59.98 50.86 61.73 0 38 40 42 44 46 48 50 52 Time (min) 54 56 58 60 62 64 A method to assist in 40 category identification Kendrick Mass Defect Plot GD1 + HexNAc 30 20 RKMD GM3 10 GD1 GM3 0 0 -‐10 -‐20 200 400 600 800 1000 1200 1400 1600 1800 2000 GM2 GM1 GM1 + Fuc -‐30 -‐40 Complex glycosphingolipids are also highly relevant to nutrition, as illustrated by interest in milk gangliosides. Internat’l J. Mass Spectrometry 305:138–150 (2011) 36 Lipidomics comes of age in nutrition and other translational sciences A. Lipidomics and Nutrition B. Examples: Sphingolipids C. Additional perspectives The lipidome is much bigger than one might have thought. Wonderful tools are on hand, but more are needed. There is much left to learn—even new compounds to be found. Potentially important discoveries are found around almost every corner. (join the fun)