A need for a 'whole-istic functional genomics' approach in complex human diseases: arthritis

Systems biology in the development of HIV vaccines

PURPOSE OF REVIEW

In the present review, we will provide the scientific rationale for applying systems biology to the development of vaccines and particularly HIV vaccines, the predictive power of systems biology on the vaccine immunological profile, the correlation between systems biology and the immunological functional profiles of different candidate vaccines, and the value of systems biology in the selection process of identifying the best-in-class candidate vaccines and in the decision process to move into in-vivo evaluation in clinical trials.

RECENT FINDINGS

Systems biology has been recently applied to the characterization of the protective yellow fever vaccine YF17D and of seasonal flu vaccines. This has been instrumental in the identification of the components of the immune response that need to be stimulated by the vaccine in order to generate protective immunity. It is worth noting that a systems biology approach is currently being performed to identify correlates of immune protection of the RV144 Thai vaccine, the only known vaccine that showed modest protection against HIV reacquisition.

SUMMARY

Systems biology represents a novel and powerful approach to predict the vaccine immunological profile, to identify the protective components of the immune response, and to help in the selection process of the best-in-class vaccines to move into clinical development.

Functionomics: the analysis of a postgenomic concept on the basis of pregenomic pharmacological studies in smooth muscle

The term functionomics (Amin 2003, Neumann et al. 2004) refers to a postgenomic integrated Systems Biology (Attur et al. 2002) using a multidimensional approach for cells, tissues and organs. It considers current or future involvement among genomics, proteomics or metabolomics, including the main factors that cause biological responses and modulation under different conditions. Our objective in the present review is to summarize the contemporary understanding of functionomics of smooth muscle pharmacology, based on the results obtained on the pregenomic era during several years in our laboratory. The present approach is based on the knowledge of the dynamics of the receptor system, which comprises a cascade of phenomena, leading from the drug administration to the final biological response. We will describe several conditions in which the final effect is modified, based on perturbations induced on drug absorption, distribution, metabolism, interaction with receptors and mobilization of second messengers, as well as by interactions with a second receptor system. We will also discuss the gaps that need to be fulfilled in order to obtain a clear and better understanding of the receptor system in smooth muscle, and to narrow the bridge between ourknowledge of the function of biological systems, genomics, and other recently introduced areas.

Technology for high-throughput screens: the present and future using zebrafish

The zebrafish is a popular vertebrate model organism with similar organ systems and gene sequences to humans. Zebrafish embryos are optically transparent enabling organ visualisation, which can be complemented with gene expression analysis at the transcript and protein levels. Furthermore, zebrafish can be treated with small molecules and drugs in a microtitre plate format for high-throughput analysis and for the identification and validation of drugs. High-throughput methodologies for use in zebrafish include phenotype-based visualisation, transcript studies using low-density DNA microarrays and proteomic analysis. These technologies offer significant whole-organism biological value in the drug discovery and drug development pipeline.