Studies of complex biological systems with applications to molecular medicine: the need to integrate transcriptomic and proteomic approaches

Abstract

Omics approaches to the study of complex biological systems with potential applications to molecular medicine are attracting great interest in clinical as well as in basic biological research. Genomics, transcriptomics and proteomics are characterized by the lack of an a priori definition of scope, and this gives sufficient leeway for investigators (a) to discern all at once a globally altered pattern of gene/protein expression and (b) to examine the complex interactions that regulate entire biological processes. Two popular platforms in "omics" are DNA microarrays, which measure messenger RNA transcript levels, and proteomic analyses, which identify and quantify proteins. Because of their intrinsic strengths and weaknesses, no single approach can fully unravel the complexities of fundamental biological events. However, an appropriate combination of different tools could lead to integrative analyses that would furnish new insights not accessible through one-dimensional datasets. In this review, we will outline some of the challenges associated with integrative analyses relating to the changes in metabolic pathways that occur in complex pathophysiological conditions (viz. ageing and altered thyroid state) in relevant metabolically active tissues. In addition, we discuss several new applications of proteomic analysis to the investigation of mitochondrial activity.

Figure 1

Categories and potential applications of proteomics and benefits of integration of proteomics and transcriptomics in the study of complex biological systems.

Figure 2

Integrated overview of the main ageing/T3-induced transcriptomic and proteomic alterations occurring in mammalian skeletal muscle. Schematic representation of the common events and mechanisms underlying the response of skeletal muscle to either ageing or T3 according to data obtained from cDNA microarray/proteomic-based studies in various mammalian models of ageing and thyroid state (mouse, rat, and human) (for details, see text and Tables 1, 2, 3, and 4).

Figure 3

Overview of the main T3-induced transcriptomic and proteomic alterations occurring in mammalian liver. Schematic representation of the alterations in gene/protein expression underlying the response of liver to T3. Schematized are the main events and mechanisms underlying the actions of T3. Summarized are data obtained in cDNA microarray/proteomic-based studies in various mammalian models (mouse, rat, and human) (for details, see text and Tables 3 and 4).