Next Article in Journal
Lipidomics-Based Comparison of Molecular Compositions of Green, Yellow, and Red Bell Peppers
Next Article in Special Issue
Data Processing Optimization in Untargeted Metabolomics of Urine Using Voigt Lineshape Model Non-Linear Regression Analysis
Previous Article in Journal
Specialized Metabolites from Ribosome Engineered Strains of Streptomyces clavuligerus
Previous Article in Special Issue
HPTLC-Based Chemical Profiling: An Approach to Monitor Plant Metabolic Expansion Caused by Fungal Endophytes
Article

Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues

1
Children’s Brain Tumour Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
2
Centre for Analytical Bioscience, Advanced Materials and Healthcare Division, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
3
National Arabidopsis Stock Centre, Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
*
Authors to whom correspondence should be addressed.
Academic Editor: Helen G. Gika
Metabolites 2021, 11(4), 240; https://doi.org/10.3390/metabo11040240
Received: 12 February 2021 / Revised: 12 April 2021 / Accepted: 12 April 2021 / Published: 14 April 2021
(This article belongs to the Special Issue Metabolomics Methodologies and Applications II)
The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme–metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill/mirVana (1:1:2); cryomill-wash/Econospin (5:1:2); rotation/phenol-chloroform (9:10:1); Sequential/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation/phenol-chloroform did not extract lipids. Cryomill/mirVana and sequential/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue. View Full-Text
Keywords: dual-extraction; cancer; metabolite; RNA; integrated omics dual-extraction; cancer; metabolite; RNA; integrated omics
Show Figures

Graphical abstract

MDPI and ACS Style

Woodward, A.; Pandele, A.; Abdelrazig, S.; Ortori, C.A.; Khan, I.; Uribe, M.C.; May, S.; Barrett, D.A.; Grundy, R.G.; Kim, D.-H.; Rahman, R. Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues. Metabolites 2021, 11, 240. https://doi.org/10.3390/metabo11040240

AMA Style

Woodward A, Pandele A, Abdelrazig S, Ortori CA, Khan I, Uribe MC, May S, Barrett DA, Grundy RG, Kim D-H, Rahman R. Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues. Metabolites. 2021; 11(4):240. https://doi.org/10.3390/metabo11040240

Chicago/Turabian Style

Woodward, Alison, Alina Pandele, Salah Abdelrazig, Catherine A. Ortori, Iqbal Khan, Marcos C. Uribe, Sean May, David A. Barrett, Richard G. Grundy, Dong-Hyun Kim, and Ruman Rahman. 2021. "Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues" Metabolites 11, no. 4: 240. https://doi.org/10.3390/metabo11040240

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop