Related Experiment Video
Updated: Feb 6, 2026
Extraction of Aqueous Metabolites from Cultured Adherent Cells for Metabolomic Analysis by Capillary Electrophoresis-Mass Spectrometry
Published on: June 9, 2019
Simultaneous Extraction of RNA and Metabolites from Single Kidney Tissue Specimens for Combined Transcriptomic and
Patrick Leuthold1, Matthias Schwab1,2,3, Ute Hofmann1
1Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany.
Abstract:
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.
Insights
This study presents a rapid protocol for simultaneous transcriptomics and metabolomics analysis from a single tissue sample. This method enhances efficiency and reproducibility for disease research using limited biopsy material.
Area of Science:
- Biochemistry
- Molecular Biology
- Genomics
Background:
- Tissue analysis is crucial for understanding disease pathophysiology.
- Heterogeneity in tissue samples, especially tumors, can complicate analysis and interpretation.
- Limited biopsy material necessitates efficient extraction methods for multiple analyses.
Purpose of the Study:
- To develop a fast and simple protocol for combined transcriptomics and metabolomics analysis from a single tissue sample.
- To enable economic use of limited biopsy material by minimizing variations.
- To validate the protocol's feasibility for investigating drug-induced alterations.
Main Methods:
- Developed a protocol for simultaneous RNA and metabolite extraction from tissue homogenates.
- Analyzed metabolites using LC-QTOF-MS after HILIC and RPLC separation.
- Applied the protocol to kidney tissue from metformin-treated mice.
Main Results:
- Achieved high reproducibility (CV ≤ 20%) for over 80% of detected metabolic features despite ion suppression.
- Demonstrated strong correlation (rₚ ≥ 0.75) between fold changes from the new protocol and an established metabolomics protocol.
- Successfully applied the combined analysis to investigate metformin-induced alterations in mouse kidney tissue.
Conclusions:
- The developed protocol offers a fast, simple, and reproducible method for combined transcriptomics and metabolomics.
- This approach maximizes the utility of limited tissue samples, reducing variability.
- The protocol is feasible for investigating molecular alterations in response to treatments or disease states.
Related Concept Videos
01:45Kidney Structure
02:18Alternative RNA Splicing
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
01:23RNA Structure
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
01:53RNA Stability
02:53Ribosomal RNA Synthesis
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
01:23RNA Interference
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...