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

Silvestri E, Lombardi A, de Lange P, Glinni D, Senese R, Cioffi F, Lanni A, Goglia F, Moreno M - J. Biomed. Biotechnol. (2010)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy.

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.

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Related in: MedlinePlus

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).
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fig2: 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).

Mentions: Biological pathways found to be changed with age in human skeletal muscle are listed in Table 1 and schematized in Figure 2. They include genes involved in the mitochondrial electron transport chain, cell cycle, and extracellular matrix. Zahn et al. [21], by comparing the transcriptional profile of ageing in muscle with previous transcriptional profiles of ageing in the kidney [22] and brain [17], found a common signature for ageing in these diverse human tissues. This common ageing signature consists of six genetic pathways; four display increased expression (genes in the extracellular matrix, genes involved in cell growth, genes encoding factors involved in complement activation, and genes encoding components of the cytosolic ribosome) and two display decreased expression in the aged muscle. These results indicate that those pathways, but not necessarily individual genes, are common elements in the age-related expression changes among different tissues [21]. This may imply that in addition to tissue-specific effects, a common ageing signature may be found in any tissue that reflects the age of the whole organism. This could have major implications for human epidemiological studies, for which frequently only blood is available.


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

Silvestri E, Lombardi A, de Lange P, Glinni D, Senese R, Cioffi F, Lanni A, Goglia F, Moreno M - J. Biomed. Biotechnol. (2010)

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).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2963870&req=5

fig2: 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).
Mentions: Biological pathways found to be changed with age in human skeletal muscle are listed in Table 1 and schematized in Figure 2. They include genes involved in the mitochondrial electron transport chain, cell cycle, and extracellular matrix. Zahn et al. [21], by comparing the transcriptional profile of ageing in muscle with previous transcriptional profiles of ageing in the kidney [22] and brain [17], found a common signature for ageing in these diverse human tissues. This common ageing signature consists of six genetic pathways; four display increased expression (genes in the extracellular matrix, genes involved in cell growth, genes encoding factors involved in complement activation, and genes encoding components of the cytosolic ribosome) and two display decreased expression in the aged muscle. These results indicate that those pathways, but not necessarily individual genes, are common elements in the age-related expression changes among different tissues [21]. This may imply that in addition to tissue-specific effects, a common ageing signature may be found in any tissue that reflects the age of the whole organism. This could have major implications for human epidemiological studies, for which frequently only blood is available.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Biologiche ed Ambientali, Università degli Studi del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy.

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.

Show MeSH
Related in: MedlinePlus