Bridging the gap between genetics and biochemistry: the science of proteomics

Scientists and researchers are well and truly engrossed with the -omics. This year’s science series reflects the current fascination with the complexity of the human body and how, alongside the various technological advances that allow us to probe the genome and epigenome,¹ the microbiome,² the metabolome,³ or the lipidome,⁴ tantalising insights are being reported into our health and ill health.

The proteome adds to this interest, representing the complete package of proteins encoded by the genome of an organism at a given time. The analysis of the proteome — proteomics — reflects the ever increasing interest in looking at the real-time functional expression of the genome in order to seek out early biomarkers of disease and develop new therapeutic strategies to combat such diseases as a result. It is little wonder that proteomics is at the forefront of the -omics revolution.

The proteome reflects the functional genome because DNA, the building blocks of life, represents the instruction manual for how to build a protein. When a protein is required, the corresponding genes go through the process of RNA transcription (which has its own –omic based on the transcriptome)5 onwards to its transport out of the cell nucleus and the process of protein translation. A new protein is born.

Our simplistic description of this process hides the startling complexity of this function and how, from the thousands of protein-encoding genes identified in the human genome, the number of proteins and their accompanying modifications and splicing are estimated to be significantly greater.

Complexity

Alongside metabolomics — the analysis of small molecule metabolites — the science of proteomics differs somewhat from the study of the genome in terms of complexity.

Notwithstanding the various epigenetic influences affecting the expression of the genome (methylation, acetylation, histone modification) and the potential influence of transposable elements of the genome (the so-called jumping genes), to look for structural point mutations or deletions, or copy number variants in the genome is a fixed process to a large extent.

Our genomes are stable and, as a result of initiatives such as the Human Genome Project,⁶ science is starting to understand more about the genetic blueprint that makes a human being.

When it comes to the analysis of the proteome, a whole new level of complexity is introduced. As well as providing a snapshot of functional gene expression, bearing in mind that we do not walk around with all our genes permanently stuck in the “on” position, when proteins are produced, they are subject to a myriad of post-translational modifications.

Many of these alterations, such as phosphorylation or methylation, are key to protein function. The identification of a specific target protein or set of proteins as biomarkers of a particular gene function or for a specific disease state, for example, must therefore take into account the ways in which that protein or proteins could be altered and the large degree of heterogeneity among people.

There are other challenges such as the differing concentrations of target species that are likely to be present and, in particular, the relatively low abundance of potentially important target molecules in the chosen media. In short, it is complicated.

The tools of the trade

Many of the challenges facing the field of proteomics are, to a large extent, being met by the amalgamation of analytical technology and computational biology (bioinformatics). The cutting edge of proteomics is represented by combining the various ways that science looks for and categorises the proteome with the statistical ways and means that the reams of data produced by such analyses are interpreted meaningfully.

It is beyond the scope of this article to provide a detailed overview of the various analytical techniques available to proteomics but some of the more widely used options include two-dimensional gel electrophoresis7 and protein microarray technology.⁸ The advent of nanotechnology and, in particular, nanotechnologies capable of reaching target proteins inside the body also represents a key advance in this field.

In keeping with its metabolomic and lipidomic cousins, proteomics is also embracing the use of mass spectrometry as a method for determining protein sequences,⁹ including matrix-assisted laser desorption/ionisation coupled with tandem mass spectrometry for peptide sequencing.¹⁰

The science behind the technology is truly a marvel as all manner of challenges are confronted according to variables as diverse as the chosen sample medium — serum or membrane proteome, for example — and how one goes about producing real-world meaningful data.

Proteomics in research action

Proteomics is big business when it comes to biomarker discovery and the interest in functional genomics. Various conditions have been examined under the banner of proteomics, none perhaps more important than its application to cancer research and the pursuit of both an early molecular signature pre-symptom onset and information about the underlying biological changes which potentially facilitate the emergence of cancer and its prognosis.

Qin and Ling¹¹ summarised some of the current literature on the proteomic study of breast cancer, for example. As per their conclusions, the full potential of proteomics has yet to be realised because the many and varied interfering variables, such as sample handling and preparation, differing analytical conditions, instruments and techniques, various stages of disease, and patient co-morbidities, which hinder the discipline remain.

Interesting is the growing acceptance that individual biomarkers for individual diseases or conditions perhaps oversimplify the complexity of human biochemistry and the challenge of discriminating a proteomic signature for condition X or condition Y. Indeed, the findings generated thus far may explain the molecular mechanisms involved in cancer and also provide a candidate biomarker or set of biomarkers.

A new wave of proteomics research activity is also starting to take an interest in this area, too. Again, using the example of cancer and how the epigenome is of potentially real interest to cancer research, Bartke and colleagues¹² discussed how proteomics is shifting its interest to this important area.

So proteomic applications looking at histone modifications and chromatin biology represent growth areas and highlight further complexity which proteomics needs to address in order to provide reproducible and meaningful results. Similar proteomic investigation into the epigenetics of neuropsychiatric disorders¹³ has begun to feature in the scientific literature, too.

Conclusions

The field of proteomics bridges the gap between genetics and biochemistry. The increasing pace of methodological and technological advance has helped to elevate proteomics to the special place in science which it now enjoys.

Although questions still remain about whether proteomics can ever fully achieve its potential, particularly with regard to reliable functional biomarkers for complex conditions and diseases, the field continues to evolve and provide some important insights into the mechanisms of disease, with the promise of so much more.

References

1. Dodou K, Whiteley P. DNA not necessarily your destiny? The growing role of epigenetics in pharmacy. The Pharmaceutical Journal 2013;290:23–4.
2. Dodou K, Whiteley P. Microbiomics: its growing significance in the world of medicines testing. The Pharmaceutical Journal 2013;290:247–8.
3. Dodou K, Whiteley P. Metabolomics: in search of biomarkers. The Pharmaceutical Journal 2013;290:512–3.
4. Dodou K, Whiteley P. Lipidomics — the science and study of how lipids affect and modify our health. The Pharmaceutical Journal 2013;291:23–4.
5. Martin JA, Wang Z. Next-generation transcriptome assembly. Nature Reviews Genetics 2011;12:671–82.
6. Guyer MS, Collins FS. The Human Genome Project and the future of medicine. The American Journal of Diseases of Children 1993;147:1145–52.
7. O’Farrell PH. High resolution two-dimensional electrophoresis of proteins. Journal of Biological Chemistry 1975;250:4007–21.
8. Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biology 2001;2:RESEARCH0004.
9. Paulo JA, Kadiyala V, Banks PA et al. Mass spectrometry-based proteomics for translational research: a technical overview. Yale Journal of Biology and Medicine 2012;85:59–73.
10. Callesen AK, Mogensen O, Jensen AK et al. Reproducibility of mass spectrometry based protein profiles for diagnosis of ovarian cancer across clinical studies: a systematic review. Journal of Proteomics 2012;75:2758–72.
11. Qin XJ, Lin BX. Proteomic studies in breast cancer. Oncology Letters 2012;3:735–43.
12. Bartke T, Borgel J, DiMaggio PA. Proteomics in epigenetics: new perspectives for cancer research. Briefings in Functional Genomics 2013;12:205–18.
13. Plazas-Mayorca MD, Vrana KE. Proteomic investigation of epigenetics in neuropsychiatric disorders: a missing link between genetics and behavior? Journal of Proteome Research 2011;10:58–65.