Limits...
Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment.

Ptitsyn A, Schlater A, Kanatous S - BMC Syst Biol (2010)

Bottom Line: Extracted RNA was hybridized on Affymetrix Human Expression chips.In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology.A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.

View Article: PubMed Central - HTML - PubMed

Affiliation: Colorado State University Department of Biology, Fort Collins, CO 80523, USA.

ABSTRACT

Background: The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (Leptonychotes weddellii) genes.

Results: Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation.

Conclusion: In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.

Show MeSH

Related in: MedlinePlus

Numbers of genes differentially expressed between age groups of Wedell seals. A-J corresponds to adult vs. juvenile; A-P corresponds to adult vs. newborn pups and J-P corresponds to juvenile vs. newborn comparisons. The largest number of differentially expressed genes was found between the adults and pups, followed by the adults and juveniles and finally the smallest number of differentially expressed genes between the pups and juveniles.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2958164&req=5

Figure 3: Numbers of genes differentially expressed between age groups of Wedell seals. A-J corresponds to adult vs. juvenile; A-P corresponds to adult vs. newborn pups and J-P corresponds to juvenile vs. newborn comparisons. The largest number of differentially expressed genes was found between the adults and pups, followed by the adults and juveniles and finally the smallest number of differentially expressed genes between the pups and juveniles.

Mentions: Analysis of canonic biological pathways, statistically overrepresented among differentially expressed genes, reveals a number of prominent biological pathways. Table 1 shows ten of the most significantly overrepresented pathways (see complete list in Supplemental Table 2, inside Additional File 1). As was expected from the previous studies on the muscle physiology of Weddell seals [1], the group of pathways most affected by age and lifestyle transformation is associated with cytoskeleton remodeling - the production of different types of muscle fibers and related signaling pathways. We have compared pairs of age groups (adults vs. newborn pups, adults vs. juveniles, and juveniles vs. newborn) and generated three lists of differentially expressed genes. These genes were found to be overlapping, with approximately half of the differential genes found on all three lists. This means that, in most cases, the difference in the patterns of gene expression between ages can be explained by the quantitative difference in activity, rather than the turning on or off behavior of certain genes or pathways. This observation is in agreement with previous studies and speaks in favor of gradual adaptation rather than the complete restructuring of metabolism with age. A Venn diagram of differential genes is presented in Figure 3. The alternative analysis of gene interaction within the lists of differentially expressed genes provides additional details (Table 2, complete lists of significant networks in Supplemental Tables 2, 3, and 4 inside Additional File 1). The overall pattern of changes with aging and lifestyle in seal skeletal muscle shows similarity to heart development and involves profound changes in cytoskeleton structure and energy metabolism. Table 2 shows the overview of differentially expressed networks of genes in most distant groups of newborn and adult seals. Comparison of similar tables for newborn versus juvenile and juvenile versus adult seals indicates that most dramatic changes in muscle metabolism happen between juvenile and adult ages and associated with adaptation to deep diving rather than aquatic life itself. Using our previous physiological studies to interpret our current data, we would have expected the greatest differences in gene expression to occur between the adults and the other two age classes. Based on the Venn diagram, that is exactly what we found. The largest number of differentially expressed genes was found between the adults and pups, followed by the adults and juveniles and finally the smallest number of differentially expressed genes between the pups and juveniles. Figure 3 shows a different aspect of the age and lifestyle-related differences. When different ages are compared by using the set of pathways statistically over-represented in each of the three lists, the thesis of quantitative differences is corroborated. The set of pathways in all ages is also similar, although there is a difference in significance as estimated by GeneGo Metacore. The p-value shown in the logarithmic scale in Figure 4 is an indicator of the signal-to-noise ratio in detecting the activity of the pathway as an entity. Assuming that the noise in all our age-to-age comparisons has the same technical nature (i.e. it comes from the same sample preparation and the same type of microarray) and scale, the over-representation of the p-value can be used to estimate the relative activity of the pathway. Subsequently, from the diagram in Figure 4 it follows that certain pathways are significantly over-represented in all age groups, while others differ in activity between pups, juveniles, and adult seals. The complete diagram of significant pathways is given in Supplemental Figure 3 (inside Additional File 1).


Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment.

Ptitsyn A, Schlater A, Kanatous S - BMC Syst Biol (2010)

Numbers of genes differentially expressed between age groups of Wedell seals. A-J corresponds to adult vs. juvenile; A-P corresponds to adult vs. newborn pups and J-P corresponds to juvenile vs. newborn comparisons. The largest number of differentially expressed genes was found between the adults and pups, followed by the adults and juveniles and finally the smallest number of differentially expressed genes between the pups and juveniles.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2958164&req=5

Figure 3: Numbers of genes differentially expressed between age groups of Wedell seals. A-J corresponds to adult vs. juvenile; A-P corresponds to adult vs. newborn pups and J-P corresponds to juvenile vs. newborn comparisons. The largest number of differentially expressed genes was found between the adults and pups, followed by the adults and juveniles and finally the smallest number of differentially expressed genes between the pups and juveniles.
Mentions: Analysis of canonic biological pathways, statistically overrepresented among differentially expressed genes, reveals a number of prominent biological pathways. Table 1 shows ten of the most significantly overrepresented pathways (see complete list in Supplemental Table 2, inside Additional File 1). As was expected from the previous studies on the muscle physiology of Weddell seals [1], the group of pathways most affected by age and lifestyle transformation is associated with cytoskeleton remodeling - the production of different types of muscle fibers and related signaling pathways. We have compared pairs of age groups (adults vs. newborn pups, adults vs. juveniles, and juveniles vs. newborn) and generated three lists of differentially expressed genes. These genes were found to be overlapping, with approximately half of the differential genes found on all three lists. This means that, in most cases, the difference in the patterns of gene expression between ages can be explained by the quantitative difference in activity, rather than the turning on or off behavior of certain genes or pathways. This observation is in agreement with previous studies and speaks in favor of gradual adaptation rather than the complete restructuring of metabolism with age. A Venn diagram of differential genes is presented in Figure 3. The alternative analysis of gene interaction within the lists of differentially expressed genes provides additional details (Table 2, complete lists of significant networks in Supplemental Tables 2, 3, and 4 inside Additional File 1). The overall pattern of changes with aging and lifestyle in seal skeletal muscle shows similarity to heart development and involves profound changes in cytoskeleton structure and energy metabolism. Table 2 shows the overview of differentially expressed networks of genes in most distant groups of newborn and adult seals. Comparison of similar tables for newborn versus juvenile and juvenile versus adult seals indicates that most dramatic changes in muscle metabolism happen between juvenile and adult ages and associated with adaptation to deep diving rather than aquatic life itself. Using our previous physiological studies to interpret our current data, we would have expected the greatest differences in gene expression to occur between the adults and the other two age classes. Based on the Venn diagram, that is exactly what we found. The largest number of differentially expressed genes was found between the adults and pups, followed by the adults and juveniles and finally the smallest number of differentially expressed genes between the pups and juveniles. Figure 3 shows a different aspect of the age and lifestyle-related differences. When different ages are compared by using the set of pathways statistically over-represented in each of the three lists, the thesis of quantitative differences is corroborated. The set of pathways in all ages is also similar, although there is a difference in significance as estimated by GeneGo Metacore. The p-value shown in the logarithmic scale in Figure 4 is an indicator of the signal-to-noise ratio in detecting the activity of the pathway as an entity. Assuming that the noise in all our age-to-age comparisons has the same technical nature (i.e. it comes from the same sample preparation and the same type of microarray) and scale, the over-representation of the p-value can be used to estimate the relative activity of the pathway. Subsequently, from the diagram in Figure 4 it follows that certain pathways are significantly over-represented in all age groups, while others differ in activity between pups, juveniles, and adult seals. The complete diagram of significant pathways is given in Supplemental Figure 3 (inside Additional File 1).

Bottom Line: Extracted RNA was hybridized on Affymetrix Human Expression chips.In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology.A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.

View Article: PubMed Central - HTML - PubMed

Affiliation: Colorado State University Department of Biology, Fort Collins, CO 80523, USA.

ABSTRACT

Background: The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (Leptonychotes weddellii) genes.

Results: Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation.

Conclusion: In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.

Show MeSH
Related in: MedlinePlus