Metabolic profiling technologies for biomarker discovery in biomedicine and drug development

LC-MS-based metabonomics analysis

Metabonomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. It has shown particular promise in the areas of toxicology and drug development, functional genomics, systems biology, and clinical diagnosis. Comprehensive metabonomics investigations are primarily a challenge for analytical chemistry. High-performance liquid chromatography-mass spectrometry (HPLC-MS) is an established technology in drug metabolite analysis and is now expanding into endogenous metabolite research. Its main advantages include wide dynamic range, reproducible quantitative analysis, and the ability to analyze biofluids with extreme molecular complexity. The aims of developing HPLC-MS for metabonomics range from understanding basic biochemistry to biomarker discovery and the structural characterization of physiologically important metabolites. In this review, the strategy and application of HPLC-MS-based metabonomics are reviewed.

LC-MS-based metabolomics in drug metabolism

Xenobiotic metabolism, a ubiquitous natural response to foreign compounds, elicits initiating signals for many pathophysiological events. Currently, most widely used techniques for identifying xenobiotic metabolites and metabolic pathways are empirical and largely based on in vitro incubation assays and in vivo radiotracing experiments. Recent work in our lab has shown that LC-MS-based metabolomic techniques are useful tools for xenobiotic metabolism research since multivariate data analysis in metabolomics can significantly rationalize the processes of xenobiotic metabolite identification and metabolic pathway analysis. In this review, the technological elements of LC-MS-based metabolomics for constructing high-quality datasets and conducting comprehensive data analysis are examined. Four novel approaches of using LC-MS-based metabolomic techniques in xenobiotic metabolism research are proposed and illustrated by case studies and proof-of-concept experiments, and the perspective on their application is further discussed.

The Edinburgh human metabolic network reconstruction and its functional analysis

A better understanding of human metabolism and its relationship with diseases is an important task in human systems biology studies. In this paper, we present a high-quality human metabolic network manually reconstructed by integrating genome annotation information from different databases and metabolic reaction information from literature. The network contains nearly 3000 metabolic reactions, which were reorganized into about 70 human-specific metabolic pathways according to their functional relationships. By analysis of the functional connectivity of the metabolites in the network, the bow-tie structure, which was found previously by structure analysis, is reconfirmed. Furthermore, the distribution of the disease related genes in the network suggests that the IN (substrates) subset of the bow-tie structure has more flexibility than other parts.

The Potential of Metabolomics Tools in Bioremediation Studies

As a post-genomics tool, metabolomics is a young and vibrant field of science in its exponential growth phase. Metabolome analysis has become very popular recently, and novel techniques for acquiring and analyzing metabolomics data continue to emerge that are useful for a variety of biological studies. The bioremediation field has a lot to gain from the advances in this emerging area. Thus, this review article focuses on the potential of various experimental and conceptual approaches developed for metabolomics to be applied in bioremediation research, such as strategies for elucidation of biodegradation pathways using isotope distribution analysis and molecular connectivity analysis, the assessment of mineralization process using metabolic footprinting analysis, and the improvement of the biodegradation process via metabolic engineering. We demonstrate how the use of metabolomics tools can significantly extend and enhance the power of existing bioremediation approaches by providing a better overview of the biodegradation process.

Application of Metabonomics in a Comparative Profiling Study Reveals N-Acetylfelinine Excretion as a Biomarker for Inhibition of the Farnesyl Pathway by Bisphosphonates

In this work, the results of metabolic profiling of urine from a preclinical comparative profiling study with the two biphosphonates ibandronate and zoledronate are reported. Toxicological assessment showed very different effects for the two compounds. Ibandronate did not cause major signs of toxicity, whereas zoledronate elicited hepatotoxicity and nephrotoxicity. Increased levels of urinary glucose and decreased levels of urinary creatinine detected by NMR also indicated drug-induced nephrotoxicity. Similarly, increased urinary levels of creatine and taurine indicated hepatotoxicity. Both organ toxicities were later confirmed by histopathology. In addition, the benefit of metabonomics as an open approach as compared to targeted methods was demonstrated by the identification of an unknown molecule in the urine of rats dosed with zoledronate. The structure elucidation revealed this molecule as N-acetylfelinine. Analysis of the pathways proposed for the biochemical synthesis of this molecule showed that the synthesis and excretion of N-acetylfelinine could easily be explained by drug-induced inhibition of farnesyl diphosphate synthase. This is the reported mode of action of bisphosphonates. Until now, N-acetylfelinine was exclusively observed in the urine of felidae species, where it is believed to be a precursor to a pheromone.

Metabolomics: current state and evolving methodologies and tools

In recent years, metabolomics developed to an accepted and valuable tool in life sciences. Substantial improvements of analytical hardware allow metabolomics to run routinely now. Data are successfully used to investigate genotype-phenotype relations of strains and mutants. Metabolomics facilitates metabolic engineering to optimise mircoorganisms for white biotechnology and spreads to the investigation of biotransformations and cell culture. Metabolomics serves not only as a source of qualitative but also quantitative data of intra-cellular metabolites essential for the model-based description of the metabolic network operating under in vivo conditions. To collect reliable metabolome data sets, culture and sampling conditions, as well as the cells' metabolic state, are crucial. Hence, application of biochemical engineering principles and method standardisation efforts become important. Together with the other more established omics technologies, metabolomics will strengthen its claim to contribute to the detailed understanding of the in vivo function of gene products, biochemical and regulatory networks and, even more ambitious, the mathematical description and simulation of the whole cell in the systems biology approach. This knowledge will allow the construction of designer organisms for process application using biotransformation and fermentative approaches making effective use of single enzymes, whole microbial and even higher cells.

Promises of Biomarkers in Drug Development ? A Reality Check

Biomarkers have been a buzz word in drug development for the last 5 years. But where do we stand now? This perspective article will demonstrate to which extent biomarkers have impacted drug development and the use of drugs. In particular, the different types of biomarkers, their identification, validation and use in different phases of drug development from drug discovery, to approval, to clinical application will be discussed as well as the state-of-the-art biomarker technologies and promising future methods. The high interest in biomarkers has generated the need for development of new technologies and refinement of existing ones. Besides discussing their perspectives of applications, the present article also illustrates the future of biomarker development in terms of qualification for regulatory use and co-development.