NMR for Metabolomics

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Mariah Simpson
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1 NMR for Metabolomics

2 NMR spectroscopy for metabonomic studies the quantitative measurement of the multi-parametric metabolic response of living systems to pathophysiological stimuli or genetic modification

3 The (Human) Pyramid of Life 1400 Chemicals Metabolomics Proteomics 3000 Enzymes Genomics 30,000 Genes

4 The (Bacterial) Pyramid of Life 761 Chemicals Metabolomics Proteomics 1152 Enzymes Genomics 4269 Genes

Sample preparations: plasma 300 μl Plasma + 300 μl buffer

5 Sample preparations: plasma 300 μl Plasma μl buffer Buffer (500 ml): 380 ml H 2 O 0.4g TSP g Na 2 HPO 4.7H 2 O 5 ml NaN 3 (4%) ph 7.4 Add H 2 O to reach 400 ml 100 ml D 2 O No centrifugation or shake to avoid bubbles and foam

6 Sample preparations: urine Centrifugation for 10 min at 6000xg 540 μl urine + 60 μl buffer Buffer: 1.5 M KH 2 PO 4 in D 2 O % TSP +0.1% NaN 3, ph 7.4

7 NMR spectroscopy 500 MHz probehead Bruker Avance III spectrometer with cryo-platform and TCI 1D 1 H gradient enhanced nuclear Overhauser enhancement spectroscopy (NOESY)-presaturation (Mixing time 10 ms) for urine 1D 1 H Carr Purcell Meiboom Gill (CPMG) echo sequence. CPMG delay of 300 ms was used with an echo time of 200 ms for plasma Temp =298K (calibrated with d 4 -Methanol), scan= 32, d1= 4s, t 1max =3.28 sec Spectral region 4.5 to 6 ppm set to zero 2D echo-antiecho [ 13 C, 1 H] HSQC. Scan=160, t 1max = 7.95 ms, t 2max = ms

8 Analysis Concentration measurement using NMR method PULCON MetaboAnalyst ( Human Metabolome Data Bank (HMDB, and Bruker database Pathway analysis was carried out using MetPA

9 Metabolomics Allows One to.. Generate metabolic signatures Monitor/measure metabolite flux Monitor enzyme/pathway kinetics Assess/identify phenotypes Monitor gene/environment interactions Track effects from toxins/perturbants Monitor consequences from gene KOs Identify functions of unknown genes

10 Traditional Metabolite Analysis HPLC, GC, CE, MS

11 Problems with Traditional Methods Requires separation followed by identification (coupled methodology) Requires optimization of separation conditions each time Often requires multiple separations Slow Manually intensive (constant supervision, high skill, tedious)

12 Advantages of NMR based metabonomic studies High Throughput High Resolution Least effort on sample preparation Changes in host metabolites Pathogen metabolites

13 NMR spectroscopy of BIOLOGICAL FLUID TYPES (primary secretory and connective roles) Key Diagnostic Fluids: Plasma Urine Saliva and other secretion

14 NMR spectroscopy of BIOLOGICAL FLUID TYPES (primary secretory and connective roles) Specialized Functions: Cerebrospinal, thyroid. Saliva (sub-lingual, parotid, submaxillary), Gastric, Bile, Pancreatic. Amniotic, Follicular, Milk, Seminal Vesicle, Prostatic, Epidydimal, Seminal. Pathological Fluids: Ascites, Cystic, Blister. Artificial Fluids: Bronchiolar lavage fluid, peritoneal dialysates, hemodialysates, fecal water, rectal dialysates, cell extracts and cell supernatants.

15 NMR spectroscopy of Human Urine (Back to 1D from the 7D world.!!!! )

16 Metabonomic by NMR spectroscopy of Human Urine

17 Metabonomic by NMR spectroscopy of Human Urine

18 Limitations of Metabonomic by 1 H NMR spectroscopy of Human Urine Small chemical shift range Spectral Crowding Analysis is biased toward high abundance metabolites

19 Application of multidimensional NMR spectroscopy and 13 C NMR for metabonomic studies. Large chemical shift range Dispersion to remove spectral crowding Takes more time for spectroscopy

20 Application of multidimensional NMR spectroscopy and 13 C NMR for metabonomic studies.

21 Application of multidimensional NMR spectroscopy and 13 C NMR for metabonomic studies samples of urine from healthy and diseased humans were collected

22 Application of multidimensional NMR spectroscopy and 13 C NMR for metabonomic studies.

23 Application of multidimensional NMR spectroscopy and 13 C NMR for metabonomic studies. Principle Component Analysis 1D peak integration taking all four metabolites 2D peak integration taking all four metabolites

24 Application of multidimensional NMR spectroscopy and 13 C NMR for metabonomic studies. Discriminant Functional Analysis Taking Betaine+TMAO from 1D data Taking TMAO from 2D data Taking Betaine from 2D data

25 Changes in metabolites as disease progresses

26 Couple them All.LC-NMR-MS

27 LC-NMR-MS

28 NMR based Metabonomics of human Biofluids as a diagnostic tool Differentially regulated metabolites during mono & co-infection of Dengue and Chikungunya Sci Rep.(2016) 6, 36833(1-12).

29 NMR based Metabonomics of human Biofluids as a diagnostic tool Differentially regulated metabolites during mono & co-infection of Dengue and Chikungunya Sci Rep.(2016) 6, 36833(1-12).

Metabolite: substance produced or used during metabolism such as lipids, sugars and amino acids

Metabolomica Analisi di biofluidi mediante spettroscopia NMR Michael Assfalg Università di Verona Terminology Metabolite: substance produced or used during metabolism such as lipids, sugars and amino acids