Systems biology meets -omic technologies: novel approaches to biomarker discovery and companion diagnostic development

Abstract

The next generation of biomarkers and companion diagnostics will require the development of technologies capable of conjugating the advances in high-throughput techniques in biology with computational methods. Systems biology is poised to contribute through an integrated view, capturing the complexity of the system, both in terms of a collection of interacting molecular components and also in terms of multiple intersecting views. Following this system-centered view, novel approaches have been developed for the identification of signatures of both disease processes and drug modes of action with the promising perspectives of better diagnosis of disease and of the discovery of more efficacious and safe drugs. The application of systems biology to the development of companion diagnostics is very recent and to date a few pioneering steps have been made in this direction. In this review, we describe the ongoing studies and the potential developments in this area of research.

Keywords:

• companion diagnostic
• molecular biomarkers
• network analysis
• systems biology
• systems medicine
• systems pharmacology

Acknowledgement

The authors are grateful to Bianca Baldacci for the graphic design contribution.

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.

Key issues

• There is an urgent need for better biomarkers to improve diagnosis, select personalized therapy and monitor therapeutic response across a wide variety of diseases.

• Several issues are still unresolved in the transfer of biomarkers from the lab to clinical practice mainly due to methodological and technological factors.

• The next generation of biomarkers and companion diagnostics could take advantage of the integration of high-throughput techniques with novel computational methods of analysis.

• Among novel computational methods are those in the field of systems biology, which combine molecular and system level knowledge typically using some form of network-based analysis.

• The application of systems biology to the field of companion diagnostics is still in its embryonic stages and new developments can be expected.

• Examples of innovations inspired by a systems biology approach are non-traditional methods for biomarker definition and analysis, and integrative analysis of multiple data modalities for diagnostic and therapeutic purposes.