What is a biomarker?
A biomarker can be defined as a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathological processes, or responses to pharmacological or other therapeutic interventions (Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework, Clin. Pharmacol. Ther., 69: 89-95, 2001).
Biomarkers include genes such as the BRCA 1/2 breast cancer susceptability genes, mutations to genes such as single nucleotide polymorphisms (SNP), proteins characteristic of a disease such as prostate specific antigen (PSA), or other molecules such as blood sugar etc. Essentially, any measurable characteristic of a biological system can be considered a biomarker.
Each type of biomarker is measured and the presence or quantity of the marker is compared to a reference range that is considered to represent normal. An example of such a range is that used in clinical monitoring of serum cholesterol level.
In simple terms, genomic analysis, the analysis of genetic information, at the DNA level may tell what could happen and analysis at the RNA level can tell what might happen in the cell. Finally, it is the proteins doing the actual work that can tell the story on what is actually happening in that cell.
In addition to conventional methods of biomarker analysis, our efforts are concentrated on a subset of molecular biomarkers that may be discovered, identified, and characterized using novel high throughput proteomic technologies such as multiplexed immunoassays and mass spectrometry.
There are approximately 30,000 genes present in the human genome that are thought to encode (can be translated into) at least ten times that many proteins. According to some estimates, the number of different protein types and forms expressed by human cells is closer to a million. These various forms of proteins may include multiple types of post-translational modifications as well as proteolytic fragments of larger proteins that potentially have significantly different biological activities than those of the parent proteins. The enormous breadth of proteins present in the proteome reflects dynamic changes in protein structure and function that occur in concert with all of the biochemical reactions going on within a cell as it performs its functions within an organism.
Some researchers believe human blood contains every protein produced by the body. So far, only a small fraction of blood proteins have been identified. A limiting factor in the comprehensive analysis of the proteome is the vast dynamic range of protein concentrations present in an organism, estimated to be on the order of 1012 or one thousand-billion fold, which complicates the analysis of low-abundance proteins in the presence of the a few highly abundant proteins that together constitute 90% of the total protein mass in human blood.
A recent report on the analysis of gene expression differences between the sexes in multiple somatic tissues of mice using microarray analysis of over 20,000 genes revealed that the extent of sexual difference in gene expression is much greater than has been previously recognized. Thousands of genes showing sexual difference exhibit highly tissue-specific patterns of expression. With virtually the same genetic code and with genome differences of less than 2% between men and women, these dramatic gender-specific differences in the expression levels of thousands of genes and the associated proteins further underline the need for the qualitative and quantitative analysis of biomarkers in health and disease.
The analysis of the proteome may reveal what actually happens in the cell and within its milieu in the body. This analysis is much more easily said than done. Proteomics is technically challenging because of both the large number of discrete protein forms and their tremendously different concentrations.
In light of these limitations it is not surprising that proteomic biomarker analyses have to date seen relatively limited applications in clinical medicine. In this arena only the most sensitive and high resolution methods can fathom the “deep proteome”, where some of the most interesting biomarkers are likely to be found. Recent progress in mass spectrometry combined with methods for selective proteome enrichment may overcome the technical limitations of identification and quantitation of non-amplified protein signals and address the most relevant questions for early diagnosis of disease and identification of biomarkers indicating optimal therapeutic interventions