Simultaneous Extraction of RNA and Metabolites from Single Kidney Tissue Specimens for Combined Transcriptomic and Metabolomic Profiling

Tissue
analysis represents a powerful tool for the investigation
of disease pathophysiology. However, the heterogeneous nature of tissue
samples, in particular of neoplastic, may affect the outcome of such
analysis and hence obscure interpretation of results. Thus, comprehensive
isolation and extraction of transcripts and metabolites from an identical
tissue specimen would minimize variations and enable the economic
use of biopsy material which is usually available in limited amounts.
Here we demonstrate a fast and simple protocol for combined transcriptomics
and metabolomics analysis in homogenates prepared from one single
tissue sample. Metabolites were recovered by protein precipitation
from lysates originally prepared for RNA isolation and were analyzed
by LC-QTOF-MS after HILIC and RPLC separation, respectively. Strikingly,
although ion suppression was observed, over 80% of the 2885 detected
metabolic features could be extracted and analyzed with high reproducibility
(CV ≤ 20%). Moreover fold changes of different tumor and nontumor
kidney tissues were correlated to an established metabolomics protocol
and revealed a strong correlation (rp ≥
0.75). In order to demonstrate the feasibility of the combined analysis
of RNA and metabolites, the protocol was applied to kidney tissue
of metformin treated mice to investigate drug induced alterations.