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Proteomics and metabolomics
PHARMACOLOGY
Proteomics and metabolomics
Learning objectives After reading this article, you should be able to: C list the most common areas of ‘omic’ investigation C appreciate the information that proteomics can provide C appreciate the information that metabolomics can provide.
David G Lambert
Abstract There has been an explosion of interest in the simultaneous study of a large number of biologically relevant molecules; the most well-known example being the study of a large number of genes or genomics with these large number of genes forming the genome. Similarly the study of the translation products of these genes; proteins (the proteome) can be investigated in proteomics and metabolic products (metabolome) in metabolomics (or metabonomics). It is possible to compare, for example, the proteome of control and diseased tissues to identify disease-related differences. This process/technology is of interest to clinicians in that it may lead to the production of novel diagnostic tests and the design of novel and even personalized therapeutics.
Proteomic often complements the genomic approaches in that the proteins measured are transcribed genomic material. The proteome provides additional information regarding post-translational modification such as phosphorylation and glycosylation and can yield important information on protein isoforms. Typical techniques used to identify proteins in proteomics are (i) 2-dimensional electrophoresis (2DE) where a mixed protein sample is separated according to charge (isoelectric point) then according to molecular weight and (ii) mass-spectrometry. A hypothetical experimental approach might be preparation of a protein sample from the muscle of a patient with malignant hyperpyrexia and a specimen of well-matched normal muscle. The samples would be subjected to 2DE and ‘spots’ that occur in the diseased but not normal tissue noted and the protein purified and then identified. The advantage of this omic approach is that many thousands of proteins can be assessed simultaneously (and information regarding interaction obtained; e.g. protein A only increases when protein B decreases). In a non-omic approach a candidate protein usually needs to be identified first then a specific assay for this candidate developed which can be screened in the disease population (in the example above for proteins A and B using this approach it is possible to identify changes in A but in reality changes in B are the more important). More recent sensitive approaches employing bottom-up proteomics methods involve enzymic digestion of protein mixtures, and then separating and sequencing the peptide fragments using liquid-chromatography coupled to a tandem mass spectrometer. The relevance to anaesthesia, critical care and pain is more than hypothetical as there have been many studies attempting to identify differences in the proteome relevant to (i) anaesthetic action, (ii) pain, (iii) sepsis and (iv) addiction.
Keywords Bioinformatics; metabolomics; proteomics
Introduction A simple MEDLINE search of omics returns many thousands of hits; so what does this all mean and is this important for anaesthesia and anaesthetists? ‘omics’ is simply the study of a very broad field and the object of that study is the ‘ome’. For example the study of genes or the genome is genomics, the study of proteins or the proteome is proteomics and the study of metabolites or the metabolome is metabolomics. Instead of analysing one gene, protein or metabolite at a time the whole genome, proteome or metabolome is analysed at once. This provides a snapshot of what is going on and clearly comparing genomes, proteomes and metabolomes from normal and diseased tissues/individuals enables the identification of differences that may lead to discovery of new disease markers, diagnostic tests or drug targets.1,2 Analysis of these complex interrelated very high-dimensional data sets usually requires bioinformatics support. The hierarchy of some of the more common ‘omic’ examples is given in Figure 1. Pharmacogenomics is covered in a separate article (see pp 374e376 of this issue).
Metabolomics1,2,5e7 Metabolomics is the study of the entire set of metabolites within a tissue including plasma, cell or an organelle. Information relating to these metabolic products complements the proteomic information described above (and see Figure 1) as the metabolites are most often produced from enzymic activity and enzymes are examples of proteins. Metabolites can also be produced as a consequence of environmental exposure (e.g. to toxins or drugs) and large-scale study of these molecules is sometimes called metabonomics. For simplicity the term metabolomics is used to describe both. Typical techniques used to identify metabolic products are (i) Gas-chromatography followed by mass-spectrometry and (ii) Liquid-chromatography followed by mass-spectrometry. In both cases the differences in the mass-
Proteomics1e4 Proteomics is the study of the entire proteome; this can be of a whole tissue (of clinical relevance this also includes plasma), cell or an organelle (e.g. purified mitochondrial preparation).
David G Lambert BSc(Hons) PhD FRCA is a Professor of Anaesthetic Pharmacology at University of Leicester, UK. Current research interests are in peptide (particularly pain and cardiovascular-related) pharmacology. Conflicts of interest: none declared.
ANAESTHESIA AND INTENSIVE CARE MEDICINE 11:9
372
Ó 2010 Elsevier Ltd. All rights reserved.
PHARMACOLOGY
Hierarchy of some of the common ‘omics’. Proteomics and metabolomics are covered in this article. (see Pharmacogenomics on pp 374–376 of this issue).
Genomics
Transcriptomics
Proteomics
Metabolomics
Transcription
Ge no me
RNA
Metabolites protein enzymes or other processes produce METABOLOME
Translation Proteins
DN A
Transcriptome Proteome
Multiple proteins interact to produce structure CELLS = cellomics TISSUES = tissuomics
Figure 1
traits. These approaches will soon leave the research laboratory and enter the clinic and possibly pave the way for personalized medicine. A
spectrometry peaks are used to identify metabolite differences between control and diseased samples. Of relevance to anaesthesia, critical care and pain many drugs used in anaesthetic practice are either specifically activated or converted to active metabolites following administration. For example the novel propofol prodrug Aquavan is converted to propofol and morphine is glucuronidated to morphine-6-glucuronide which has higher potency than the parent morphine. In addition a large number of drugs are metabolized by members of the cytochrome P450 family (that can be studied using proteomic approaches) and the action of remifentanyl is terminated by cholinesterase. The metabolic pathways (in the form of metabolites) for all of these agents can be studied using metabolomic approaches and the metabolome following the use of novel drug molecules can be examined allowing metabolite related side effect profiles to be predicted.
REFERENCES 1 Joyce AR, Palsson BØ. The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell Biol 2006; 7: 198e210. 2 Omics Gateway, http://www.nature.com/omics/index.html 3 Open Proteomics Database, http://bioinformatics.icmb.utexas.edu/ OPD/ 4 Niederberger E, Geisslinger G. Proteomics in neuropathic pain research. Anesthesiology 2008; 108: 314e23. 5 Nicholson JK, Wilson ID. Understanding ‘global’ systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2003; 2: 668e76. 6 Ramautar R, van der Plas AA, Nevedomskaya E, et al. Explorative analysis of urine by capillary electrophoresis-mass spectrometry in chronic patients with complex regional pain syndrome. J Proteome Res 2009; 8: 5559e67. 7 Human Metabolome Database, http://www.hmdb.ca/
Summary Omic science(s) should not be considered singly but rather as complementary-interacting approaches to address complex phenotypic (e.g. predisposition to disease and drug response)
ANAESTHESIA AND INTENSIVE CARE MEDICINE 11:9
373
Ó 2010 Elsevier Ltd. All rights reserved.
Proteomics and metabolomics
Learning objectives After reading this article, you should be able to: C list the most common areas of ‘omic’ investigation C appreciate the information that proteomics can provide C appreciate the information that metabolomics can provide.
David G Lambert
Abstract There has been an explosion of interest in the simultaneous study of a large number of biologically relevant molecules; the most well-known example being the study of a large number of genes or genomics with these large number of genes forming the genome. Similarly the study of the translation products of these genes; proteins (the proteome) can be investigated in proteomics and metabolic products (metabolome) in metabolomics (or metabonomics). It is possible to compare, for example, the proteome of control and diseased tissues to identify disease-related differences. This process/technology is of interest to clinicians in that it may lead to the production of novel diagnostic tests and the design of novel and even personalized therapeutics.
Proteomic often complements the genomic approaches in that the proteins measured are transcribed genomic material. The proteome provides additional information regarding post-translational modification such as phosphorylation and glycosylation and can yield important information on protein isoforms. Typical techniques used to identify proteins in proteomics are (i) 2-dimensional electrophoresis (2DE) where a mixed protein sample is separated according to charge (isoelectric point) then according to molecular weight and (ii) mass-spectrometry. A hypothetical experimental approach might be preparation of a protein sample from the muscle of a patient with malignant hyperpyrexia and a specimen of well-matched normal muscle. The samples would be subjected to 2DE and ‘spots’ that occur in the diseased but not normal tissue noted and the protein purified and then identified. The advantage of this omic approach is that many thousands of proteins can be assessed simultaneously (and information regarding interaction obtained; e.g. protein A only increases when protein B decreases). In a non-omic approach a candidate protein usually needs to be identified first then a specific assay for this candidate developed which can be screened in the disease population (in the example above for proteins A and B using this approach it is possible to identify changes in A but in reality changes in B are the more important). More recent sensitive approaches employing bottom-up proteomics methods involve enzymic digestion of protein mixtures, and then separating and sequencing the peptide fragments using liquid-chromatography coupled to a tandem mass spectrometer. The relevance to anaesthesia, critical care and pain is more than hypothetical as there have been many studies attempting to identify differences in the proteome relevant to (i) anaesthetic action, (ii) pain, (iii) sepsis and (iv) addiction.
Keywords Bioinformatics; metabolomics; proteomics
Introduction A simple MEDLINE search of omics returns many thousands of hits; so what does this all mean and is this important for anaesthesia and anaesthetists? ‘omics’ is simply the study of a very broad field and the object of that study is the ‘ome’. For example the study of genes or the genome is genomics, the study of proteins or the proteome is proteomics and the study of metabolites or the metabolome is metabolomics. Instead of analysing one gene, protein or metabolite at a time the whole genome, proteome or metabolome is analysed at once. This provides a snapshot of what is going on and clearly comparing genomes, proteomes and metabolomes from normal and diseased tissues/individuals enables the identification of differences that may lead to discovery of new disease markers, diagnostic tests or drug targets.1,2 Analysis of these complex interrelated very high-dimensional data sets usually requires bioinformatics support. The hierarchy of some of the more common ‘omic’ examples is given in Figure 1. Pharmacogenomics is covered in a separate article (see pp 374e376 of this issue).
Metabolomics1,2,5e7 Metabolomics is the study of the entire set of metabolites within a tissue including plasma, cell or an organelle. Information relating to these metabolic products complements the proteomic information described above (and see Figure 1) as the metabolites are most often produced from enzymic activity and enzymes are examples of proteins. Metabolites can also be produced as a consequence of environmental exposure (e.g. to toxins or drugs) and large-scale study of these molecules is sometimes called metabonomics. For simplicity the term metabolomics is used to describe both. Typical techniques used to identify metabolic products are (i) Gas-chromatography followed by mass-spectrometry and (ii) Liquid-chromatography followed by mass-spectrometry. In both cases the differences in the mass-
Proteomics1e4 Proteomics is the study of the entire proteome; this can be of a whole tissue (of clinical relevance this also includes plasma), cell or an organelle (e.g. purified mitochondrial preparation).
David G Lambert BSc(Hons) PhD FRCA is a Professor of Anaesthetic Pharmacology at University of Leicester, UK. Current research interests are in peptide (particularly pain and cardiovascular-related) pharmacology. Conflicts of interest: none declared.
ANAESTHESIA AND INTENSIVE CARE MEDICINE 11:9
372
Ó 2010 Elsevier Ltd. All rights reserved.
PHARMACOLOGY
Hierarchy of some of the common ‘omics’. Proteomics and metabolomics are covered in this article. (see Pharmacogenomics on pp 374–376 of this issue).
Genomics
Transcriptomics
Proteomics
Metabolomics
Transcription
Ge no me
RNA
Metabolites protein enzymes or other processes produce METABOLOME
Translation Proteins
DN A
Transcriptome Proteome
Multiple proteins interact to produce structure CELLS = cellomics TISSUES = tissuomics
Figure 1
traits. These approaches will soon leave the research laboratory and enter the clinic and possibly pave the way for personalized medicine. A
spectrometry peaks are used to identify metabolite differences between control and diseased samples. Of relevance to anaesthesia, critical care and pain many drugs used in anaesthetic practice are either specifically activated or converted to active metabolites following administration. For example the novel propofol prodrug Aquavan is converted to propofol and morphine is glucuronidated to morphine-6-glucuronide which has higher potency than the parent morphine. In addition a large number of drugs are metabolized by members of the cytochrome P450 family (that can be studied using proteomic approaches) and the action of remifentanyl is terminated by cholinesterase. The metabolic pathways (in the form of metabolites) for all of these agents can be studied using metabolomic approaches and the metabolome following the use of novel drug molecules can be examined allowing metabolite related side effect profiles to be predicted.
REFERENCES 1 Joyce AR, Palsson BØ. The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell Biol 2006; 7: 198e210. 2 Omics Gateway, http://www.nature.com/omics/index.html 3 Open Proteomics Database, http://bioinformatics.icmb.utexas.edu/ OPD/ 4 Niederberger E, Geisslinger G. Proteomics in neuropathic pain research. Anesthesiology 2008; 108: 314e23. 5 Nicholson JK, Wilson ID. Understanding ‘global’ systems biology: metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2003; 2: 668e76. 6 Ramautar R, van der Plas AA, Nevedomskaya E, et al. Explorative analysis of urine by capillary electrophoresis-mass spectrometry in chronic patients with complex regional pain syndrome. J Proteome Res 2009; 8: 5559e67. 7 Human Metabolome Database, http://www.hmdb.ca/
Summary Omic science(s) should not be considered singly but rather as complementary-interacting approaches to address complex phenotypic (e.g. predisposition to disease and drug response)
ANAESTHESIA AND INTENSIVE CARE MEDICINE 11:9
373
Ó 2010 Elsevier Ltd. All rights reserved.