Publications

@article{Woodward2021-wy,

title = {Integrated metabolomics and transcriptomics using an optimised 

 dual extraction process to study human brain cancer cells and 

 tissues},

author = {Alison Woodward and Alina Pandele and Salah Abdelrazig and Catherine A Ortori and Iqbal Khan and Marcos Castellanos Uribe and Sean May and David A Barrett and Richard G Grundy and Dong-Hyun Kim and Ruman Rahman},

year  = {2021},

date = {2021-04-01},

journal = {Metabolites},

volume = {11},

number = {4},

pages = {240},

publisher = {MDPI AG},

abstract = {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.},

keywords = {Cancer, dual-extraction, integrated omics, metabolite, RNA},

pubstate = {published},

tppubtype = {article}

}