The challenge facing researchers may surpass that of mapping the human genome. Interpreting proteomics is infinitely more complex than that of nucleic acids. The shift in focus has also sent a message out to manufacturers of lab equipment, which has needed to show capability of adapting to higher complexity and fragility of the human proteome.
Technology to detect protein-based biomarkers has advanced in leaps and bounds, with high levels of technological advancements already visible across instruments such as mass spectrometers, microarrays, and 2D gel electrophoresis equipment, all increasing throughput. Enhanced automation is also having a profound impact on biomarker discovery.
Biomarkers would help in targeting the appropriate medicine to the patients, thereby increasing the chances of recovery and reducing the side effects of medications. The hope now is drugs can eventually be developed that prove effective against Alzheimer's and Parkinson's disease.
In particular, clinical diagnostics capable of early detection of cancers are likely to surface soon. Biomarkers include CA 125 for ovarian cancer, CA 15-3 for breast cancer, CEA for ovarian, lung, breast, pancreas, and GI tract cancers, and PSA for prostate cancer.
One major obstacle that scientists will be forced to confront is the relative difficulty in resolution and purification of protein mixtures, magnifying the overall problem of the separation process.
The report, produced by Technical Insights, forces the pharmaceutical industry to confront the issues sooner rather than later. Its analyst Ravi Shankar said: "Protein molecules have different structures and chemical properties and also vary with respect to their intracellular abundance in different cell types."
"It is therefore virtually impossible to find an analytical technique that is capable of resolving and separating the thousands of protein forms present in a cell at a given time."
The report cites legislation as a key industry driver that will determine the fortunes of proteomics. Stringent regulations set by controlling bodies such as the Food and Drug Administration (FDA) in the United States concerning the validity of biomarkers and approval of drugs or diagnostic tests that are being developed by utilizing them.
Legislation concerning biomarker validation is a big challenge facing pharmaceutical companies. With regulations requiring validation and authenticity of biomarker-based drugs/tests, ever-shrinking budgets are sure to be tested to the limit. Validation is a costly and time-consuming process and involves testing the drug or diagnostic kit on numerous individuals, all without the guarantee of ever reaching the market.
Biomarkers could be considered the lifeline of pharmaceutical companies. They help to select suitable patients for participation in clinical trials besides enabling toxicity profiling.
"By reviewing the drugs' toxicity profile by employing biomarkers, pharmaceuticals companies can retain or drop the drug at the initial stage of development itself, and thereby, avoid spending precious resources on drug candidates that may prove to be unviable at a later stage of development," Shankar added.
As biomarkers gain in prominence, developers of biomarker-based tests have to ensure that their tests are included in the screening guidelines promulgated by authoritative bodies. Unless this is done, market uptake is likely to be limited as patients are expected to resist spending their own money on these expensive tests.
The sensitivity and specificity of biomarker-based screening is likely to be a challenge that will need attention. One way is by developing tests that employ multiple biomarkers rather than relying on tests with a solo biomarker.
The report concludes that the shift in focus from discovering genomic biomarkers to protein biomarkers, are driving demand for robust research instruments that enable multiplexing and reduce manual steps such as sample preparation.
Companies developing flexible, low-cost, biochips for gene and protein expression profiling and microfluidics-based platforms are expected to profit, providing further momentum to the discovery of new biomarkers and their use in clinical diagnostics and drug development.