Pairwise metabolite-metabolite correlation analysis (MMCA) of HR-MAS 1H NMR spectra from 407 human brain tumours
Basetti Madhu1, Sean McGuire1, Alexandra Jauhiainen2, and John R Griffiths1

1Molecular Imaging (MRI & MRS), Cancer Research UK Cambridge Institute, Cambridge, United Kingdom, 2Early Clinical Biometrics, AstraZeneca AB R&D, Molndal, Sweden

Synopsis

Human brain tumour tissues from glioblastoma multiforme, astrocytoma, meningioma, oligodendroglioma and metastatic tumours were analyzed by metabolite-metabolite correlation analysis of HRMAS 1H NMR spectra from the eTumour database. The following metabolites were quantified using a modified LC-Model basis set: alanine (Ala), choline (Cho), creatine (Cr), lactate (Lac), glutamine (Gln), glutamate (Glu), glycine (Glyn), N-acetylaspartate (NAA), phosphocholine (PCh), phosphocreatine (PCr), taurine (tau), myo-inositol (Ino) and various lipids/macromolecules. The estimated metabolite concentrations from LCModel fittings were used in the investigation of pairwise metabolite-metabolite correlations. Pairwise metabolite-metabolite correlations can serve as an overview of metabolism and can be helpful in understanding the cellular metabolism.

Purpose

Human brain tumour tissues from glioblastoma multiforme, astrocytoma, meningioma, oligodendroglioma and metastatic tumours were analyzed by metabolite-metabolite correlation analysis of HRMAS 1H NMR spectra from the eTumour database. The following metabolites were quantified using a modified LC-Model basis set: alanine (Ala), choline (Cho), creatine (Cr), lactate (Lac), glutamine (Gln), glutamate (Glu), glycine (Glyn), N-acetylaspartate (NAA), phosphocholine (PCh), phosphocreatine (PCr), taurine (tau), myo-inositol (Ino) and various lipids/macromolecules. The estimated metabolite concentrations from LCModel fittings were used in the investigation of pairwise metabolite-metabolite correlations analysis (MMCA). Pairwise metabolite-metabolite correlations can serve as an overview of metabolism and can be helpful in understanding the cellular metabolism.

Materials and Methods

All the HRMAS 1H NMR spectral data (water pre-saturated and 30ms T2 filtered (CPMG) spectra) were downloaded from the e-Tumour database1.The eTumour project (2004 – 2009), funded by the EU (FP6-2002-LIFESCIHEALTH 503094), involved 11 partners across Europe and Argentina. Spectra of tumour tissue samples from verified cases of glioblastoma multiforme (GBM, n=154), astrocytoma (ASTR, n=107), meningioma (MENI, n=75) , oligodendroglioma (ODG, n=37 and brain metastasis (MET, n=34) were analysed in this study. T2 filtered (30ms in CPMG) HRMAS 1H NMR spectra was used for PCA analysis. Spectra data was binned with 0.01ppm interval between 0.5 ppm to 4.5 ppm (AMIX). SIMCA 14 (Umetrics) was used for the PCA analysis. LCModel was used with a modified basis set to estimate the metabolite concentrations from water suppressed-spectra; alanine, choline, creatine, lactate, glutamine, glutamate, NAA, phosphocholine, taurine, myo-inositol and lipids/macromolecules were quantifiable. The pairwise metabolite-metabolite correlations were estimated by using a mixed model method we recently developed2 ; it also highlights correlations with high significance at a cut-off value of P ≤ 0.001.

Results and Discussion

Many positive correlations were observed between the metabolites belonging to the same biochemical pathway, and also between other metabolites in different biochemical modules.There were many negative correlations between lipids and the small-molecule metabolites involved in glycolysis, energy metabolism, membrane metabolism and glutamine and glutamate metabolism (Fig 3). A positive correlation between lactate and alanine was observed in all brain tumour types except ODG. An upregulation of glycolysis (the Warburg effect) in these tumours might be the cause for this observation. The choline plus creatine level was previously found to be negatively correlated with lipid levels in human brain tumours from in vivo MRS spectral data3. This was attributed to dilution of metabolite levels due to a heterogeneous mix of tissues, tumour grades, inflammation, hypoxia and necrosis3. Lipid and glutamine levels from in vivo 1H MRS data had shown a negative correlation in paediatric brain tumours4. It has also been shown that a positive correlation between signals at 1.3ppm and lipid pseudo-droplets5 (and also lipids6) in human brain tumour tissues consisting of no-necrosis, low necrosis and high necrosis. The negative correlation between various metabolites and lipids observed in this ex vivo study shows further evidence of these effects. ODG tumours showed a set of different correlations within the metabolites when compared to the correlation data of other brain tumour types (table 1).The PCh to GPC ratio is regarded a marker of malignancy7. The plot of these metabolites showed a strong positive correlation in MENI, whereas in GBM and ASTR there was no correlation (table 1).

Conclusion

HRMAS 1H NMR spectral data of brain tumour tissues shows numerous negative correlations between the signals of metabolites and of lipids, perhaps because the tissue samples include volumes with different tumour grades, inflammation, hypoxia and necrosis. The positive correlation observed between lactate and alanine levels in all brain tumours in this study (with an exception of ODG) might be due to enhanced glycolysis. Detection of the percentage of necrosis in human brain tumours is important for estimating grade of malignancy and also the response to therapy. In future work we will therefore analyse the in vivo 1H MRS spectra in the eTumour database and compare them with the HRMAS 1H NMR metabolite data. MMCA can be a helpful tool in understanding tumour metabolism.

Acknowledgements

This work was supported by Cancer Research UK. We acknowledge our gratitude to all the groups and members of the eTumour project and special thanks to Dr Margarida Julià-Sapé, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Spain for her help with accessing the database.

References

1. Julià-Sapé M, Lurgi M, Mier M, et al. Strategies for annotation and curation of translational databases: the eTUMOUR project. Database (Oxford). 2012 Nov 22;2012:bas035.
2. Jauhiainen A, Madhu B, Narita M, et al. Normalization of metabolomics data with applications to correlation maps. Bioinformatics. 2014 30:2155-61.
3. Howe FA1, Barton SJ, Cudlip SA, Stubbs M, Saunders DE, Murphy M, Wilkins P, Opstad KS, Doyle VL, McLean MA, Bell BA, Griffiths JR. Metabolic profiles of human brain tumors using quantitative in vivo 1H magnetic resonance spectroscopy. Magn Reson Med. 2003 Feb;49(2):223-32.
4. Wilson M, Cummins CL, Macpherson L, Sun Y, Natarajan K, Grundy RG, Arvanitis TN, Kauppinen RA, Peet AC. Magnetic resonance spectroscopy metabolite profiles predict survival in paediatric brain tumours. Eur J Cancer. 2013 Jan;49(2):457-64.
5. Opstad KS, Bell BA, Griffiths JR, Howe FA. An investigation of human brain tumour lipids by high-resolution magic angle spinning 1H MRS and histological analysis. NMR Biomed. 2008 21: 677-85.
6. Cheng LL, Anthony DC, Comite AR, Black PM, Tzika AA, Gonzalez RG. Quantification of micro heterogeneity in glioblastoma multiforme with ex vivo high-resolution magic-angle spinning (HRMAS) proton magnetic resonance spectroscopy. Neuro Oncol. 2000 Apr;2(2):87-95.
7. Aboagye EO, Bhujwalla ZM. Malignant transformation alters membrane choline phospholipid metabolism of human mammary epithelial cells. Cancer Res. 1999 Jan 1;59(1):80-4.

Figures

Figure 1. MR images and corresponding H&E sections

Figure 2. PCA scores and loadings plots from 30ms T2 filtered (CPMG) HRMAS 1H NMR data from Brain tumour tumour tissues. Samples in Scores plot are 1.GBM(green), 2.Astrocytoma(violet), 3.Meningioma(red), 4.ODG(yesllow), 5.Metastatsis(blue).

Figure 3. Pairwise metabolite-metabolite correlations in brain tumour tissues. Colour key shows the correlation coefficients

Table 1. Pairwise metabolite-metabolite correlations in brain tumour tissues.



Proc. Intl. Soc. Mag. Reson. Med. 24 (2016)
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