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A Brief Introduction to Metabolomics

Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).

Metabolome refers to the complete set of chemical compounds involved in an organism's metabolism (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites)
Metabolomics is the scientific study of chemical processes involving metabolites. Metabolomics is a relatively new member to the ‘-omics’ family of systems biology technologies.

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A Brief Introduction to Metabolomics

  1. 1. Metabolomics Metabolite : 1. These are organic compounds that are used in/created by, the chemical reactions happening in every cell of living organisms. 2. These are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. 3. These have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones). Metabolome : It refers to the complete set of chemical compounds involved in an organism's metabolism (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) Ranjith Raj Vasam, PG - Bioinformatics ranjith.raj@students.iiit.ac.in
  2. 2. Metabolomics Metabolomics : • It is the scientific study of chemical processes involving metabolites. Metabolomics is a relatively new member to the ‘-omics’ family of systems biology technologies. • Metabolomics aims to compare the relative differences between biological samples based on their metabolite profiles. • It can provide an instantaneous snapshot of the entire physiology of an organism. • Emerging field of metabolomics combines strategies to identify and quantify cellular metabolites using sophisticated analytical technologies with the application of statistical and multi-variant methods for information extraction and data interpretation. • Huge progress was made in the last two decades, in the sequencing of a number of different organisms. • Simultaneously, large investments were made to develop analytical approaches to analyze the different cell products, such as those from gene expression (transcripts), proteins, and metabolites. • All of these so-called ‘omics' approaches, including genomics, transcriptomics, proteomics, and metabolomics, are considered important tools to be applied and utilized to understand the biology of an organism and its response to environmental stimuli or genetic perturbation. • Due to the huge diversity of chemical structures and the large differences in abundance, there is no single technology available to analyze the entire metabolome. • Therefore, a number of complementary approaches have to be established for extraction, detection, quantification, and identification of as many metabolites as possible. Ranjith Raj Vasam, PG - Bioinformatics ranjith.raj@students.iiit.ac.in
  3. 3. Metabolomics Challenges in metabolomics include extraction of information and to interpret it in a biological context from the vast amount of data produced by high-throughput analyzers. Application of sophisticated statistical and multi-variant data analysis tools, including cluster analysis, pathway mapping, comparative overlays, and heatmaps has demonstrated that current thinking needs to change to deal with large data sets and distinguish between noise and real sample-related information. Combating Data Overload : Indeed, metabolomicists are being swamped by data. Research says it can name about 400 metabolites in 25 minutes from a single run. "But typically there are another 500 to 1,000 compounds there that we don't recognize. In case, If you're working with the human genome, you see 20,000 genes and you're done. But there are about 200,000 known metabolites, and it's a good guess to say that there are at least a million out there." Industry and Research groups are investing in writing and perfecting algorithms to search mass spectra for unknown metabolites and record them as in a library. Hopefully, the program might sift through 500,000 spectra in 24 hours, compared to the 500 could be managed manually. Recurring metabolic patterns can still yield statistically useful indicators even if the compounds themselves can't be identified. Commercially available pattern-recognition software does a competent job, although most researchers still write their own programs to move data from their equipment into their statistical analysis software. Right now, we're in a period similar to the early days of DNA sequencing. In the beginning, the sequencing was done by hand. As the process was better and better understood, sequencing was not only more and more automated, but there also was more confidence that the software was doing it correctly. In metabolomics, we're still spending a fair amount of time checking the machines and software. A few years from now, the process will be automated and very straightforward." Ranjith Raj Vasam, PG - Bioinformatics ranjith.raj@students.iiit.ac.in
  4. 4. Metabolomics Key Applications Personalised medicine : In healthcare, we currently use classical biochemical tests to measure individual metabolite concentrations to identify disease states (e.g. the blood- glucose level in the case of diabetes). Metabolomics offers the potential for the rapid indentification of hundreds of metabolites, enabling us to identify these disease states much earlier. Thus, Personalised medicine, the ultimate customisation of healthcare, requires metabolomics for quick medical diagnosis to identify disease. Nutrigenomics[It is a generalised term which links genomics, transcriptomics, proteomics and metabolomics to human nutrition.] : In general a metabolome in a given body fluid is influenced by endogenous factors such as age, sex, body composition and genetics as well as underlying pathologies. The large bowel microflora are also a very significant potential confounder of metabolic profiles and could be classified as either an endogenous or exogenous factor. The main exogenous factors are diet and drugs. Diet can then be broken down to nutrients and non- nutrients. Metabolomics is one means to determine a biological endpoint, or metabolic fingerprint, which reflects the balance of all these forces on an individual's metabolism. Agricultural : Metabolomics enables us to improve genetically modified plants, and helps us to estimate associated risks by allowing us to get a glimpse of their complex biochemistry via informative snapshots acquired at different time points during plant development. Functional Genomics : Metabolomics can be an excellent tool for determining the phenotype caused by a genetic manipulation, such as gene deletion or insertion. Sometimes this can be a sufficient goal in itself—for instance, to detect any phenotypic changes in a genetically modified plant intended for human or animal consumption. More exciting is the prospect of predicting the function of unknown genes by comparison with the metabolic perturbations caused by deletion/insertion of known genes. Toxicology(/Toxicity assessment) : Metabolic profiling (especially of urine or blood plasma samples) detects the physiological changes caused by toxic insult of a chemical(s). In many cases, the observed changes can be related to specific syndromes, e.g. a specific lesion in liver or kidney. This is of particular relevance to pharmaceutical companies wanting to test the toxicity of potential drug candidates: “ if a compound can be eliminated before it reaches clinical trials on the grounds of adverse toxicity, it saves the enormous expense of the trials. “ Ranjith Raj Vasam, PG - Bioinformatics ranjith.raj@students.iiit.ac.in
  5. 5. Metabolomics Biomarker discovery : In metabolomics, biomarkers are small molecules (metabolites) that can be used to distinguish two groups of samples, typically a disease and control group. For example, a metabolite reliably present in disease samples, but not in healthy individuals would be classed as a biomarker. Samples of urine, saliva, bile, or seminal fluid contain highly informative metabolites, and can be readily analysed through metabolomics fingerprinting or profiling, for the purpose of biomarker discovery. Conclusion Metabolomics represents the interface between genetic pre-disposition and environmental influence. It is because of this unique position in the systems biology hierarchy that metabolomics could prove invaluable in our quest to understand the function of genes, to be able to control and/or design novel organisms that may benefit our health or lifestyles, and to understand more fully the molecular physiology of ourselves and that of other organisms. References : 1.Metabolomics : An Official Journal of the Metabolomics Society http://link.springer.com/journal/11306 2. http://whatis.techtarget.com/definition/metabolomics 3.http://metabolomics.chem.agilent.com/ 4.http://www.biotechniques.com/BiotechniquesJournal/specialissues/2009/April/What-is- metabolomics-all-about/biotechniques-140692.html 5.http://www.the-scientist.com/?articles.view/articleNo/16400/title/Growing-Pains-for- Metabolomics/ 6. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613217/ Ranjith Raj Vasam, PG - Bioinformatics ranjith.raj@students.iiit.ac.in

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