Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity

Jatin G. Burniston, Jenna Kenyani, Donna Gray, Eleonora Guadagnin, Ian H. Jarman, James N. Cobley, Daniel J. Cuthbertson, Yi-Wen Chen, Jonathan M. Wastling, Paulo J. Lisboa, Lauren G. Koch, Steven L. Britton

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Abstract

Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features.
Biological significanceQuantitative proteome profiling revealed that there is little or no sexual dimorphism in the skeletal muscle response to artificial selection on running capacity. Instead we found that noncanonical STAT3 signalling may be associated with low exercise capacity and skeletal muscle insulin resistance. Importantly, this discovery was made using unsupervised multivariate association mapping and bibliometric network analyses. This allowed our interpretation of the findings to be guided by patterns within the data rather than our preconceptions about which proteins or processes are of greatest interest. Moreover, we demonstrate that this novel approach can be applied to 2D gel analysis, which is unsurpassed in its ability to profile protein species but currently has few dedicated bioinformatic tools.
Original languageEnglish
Pages (from-to)230-245
Number of pages16
JournalJournal of Proteomics
Volume106
Early online date24 Apr 2014
DOIs
Publication statusPublished - 25 Jun 2014

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Muscles
Proteins
Bibliometrics
Skeletal Muscle
Computational Biology
Protein Disulfide-Isomerases
STAT3 Transcription Factor
Electrophoresis, Gel, Two-Dimensional
Proteome
Post Translational Protein Processing
Sex Characteristics
Running
Insulin Resistance
Western Blotting
Gels
Genes

Cite this

Burniston, J. G., Kenyani, J., Gray, D., Guadagnin, E., Jarman, I. H., Cobley, J. N., ... Britton, S. L. (2014). Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity. Journal of Proteomics, 106, 230-245. https://doi.org/10.1016/j.jprot.2014.04.015
Burniston, Jatin G. ; Kenyani, Jenna ; Gray, Donna ; Guadagnin, Eleonora ; Jarman, Ian H. ; Cobley, James N. ; Cuthbertson, Daniel J. ; Chen, Yi-Wen ; Wastling, Jonathan M. ; Lisboa, Paulo J. ; Koch, Lauren G. ; Britton, Steven L. / Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity. In: Journal of Proteomics. 2014 ; Vol. 106. pp. 230-245.
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abstract = "Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10{\%}) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features.Biological significanceQuantitative proteome profiling revealed that there is little or no sexual dimorphism in the skeletal muscle response to artificial selection on running capacity. Instead we found that noncanonical STAT3 signalling may be associated with low exercise capacity and skeletal muscle insulin resistance. Importantly, this discovery was made using unsupervised multivariate association mapping and bibliometric network analyses. This allowed our interpretation of the findings to be guided by patterns within the data rather than our preconceptions about which proteins or processes are of greatest interest. Moreover, we demonstrate that this novel approach can be applied to 2D gel analysis, which is unsurpassed in its ability to profile protein species but currently has few dedicated bioinformatic tools.",
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Burniston, JG, Kenyani, J, Gray, D, Guadagnin, E, Jarman, IH, Cobley, JN, Cuthbertson, DJ, Chen, Y-W, Wastling, JM, Lisboa, PJ, Koch, LG & Britton, SL 2014, 'Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity', Journal of Proteomics, vol. 106, pp. 230-245. https://doi.org/10.1016/j.jprot.2014.04.015

Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity. / Burniston, Jatin G.; Kenyani, Jenna; Gray, Donna; Guadagnin, Eleonora; Jarman, Ian H.; Cobley, James N.; Cuthbertson, Daniel J.; Chen, Yi-Wen; Wastling, Jonathan M.; Lisboa, Paulo J.; Koch, Lauren G.; Britton, Steven L.

In: Journal of Proteomics, Vol. 106, 25.06.2014, p. 230-245.

Research output: Contribution to journalArticle

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T1 - Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity

AU - Burniston, Jatin G.

AU - Kenyani, Jenna

AU - Gray, Donna

AU - Guadagnin, Eleonora

AU - Jarman, Ian H.

AU - Cobley, James N.

AU - Cuthbertson, Daniel J.

AU - Chen, Yi-Wen

AU - Wastling, Jonathan M.

AU - Lisboa, Paulo J.

AU - Koch, Lauren G.

AU - Britton, Steven L.

PY - 2014/6/25

Y1 - 2014/6/25

N2 - Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features.Biological significanceQuantitative proteome profiling revealed that there is little or no sexual dimorphism in the skeletal muscle response to artificial selection on running capacity. Instead we found that noncanonical STAT3 signalling may be associated with low exercise capacity and skeletal muscle insulin resistance. Importantly, this discovery was made using unsupervised multivariate association mapping and bibliometric network analyses. This allowed our interpretation of the findings to be guided by patterns within the data rather than our preconceptions about which proteins or processes are of greatest interest. Moreover, we demonstrate that this novel approach can be applied to 2D gel analysis, which is unsurpassed in its ability to profile protein species but currently has few dedicated bioinformatic tools.

AB - Profiling of protein species is important because gene polymorphisms, splice variations and post-translational modifications may combine and give rise to multiple protein species that have different effects on cellular function. Two-dimensional gel electrophoresis is one of the most robust methods for differential analysis of protein species, but bioinformatic interrogation is challenging because the consequences of changes in the abundance of individual protein species on cell function are unknown and cannot be predicted. We conducted DIGE of soleus muscle from male and female rats artificially selected as either high- or low-capacity runners (HCR and LCR, respectively). In total 696 protein species were resolved and LC–MS/MS identified proteins in 337 spots. Forty protein species were differentially (P < 0.05, FDR < 10%) expressed between HCR and LCR and conditional independence mapping found distinct networks within these data, which brought insight beyond that achieved by functional annotation. Protein disulphide isomerase A3 emerged as a key node segregating with differences in aerobic capacity and unsupervised bibliometric analysis highlighted further links to signal transducer and activator of transcription 3, which were confirmed by western blotting. Thus, conditional independence mapping is a useful technique for interrogating DIGE data that is capable of highlighting latent features.Biological significanceQuantitative proteome profiling revealed that there is little or no sexual dimorphism in the skeletal muscle response to artificial selection on running capacity. Instead we found that noncanonical STAT3 signalling may be associated with low exercise capacity and skeletal muscle insulin resistance. Importantly, this discovery was made using unsupervised multivariate association mapping and bibliometric network analyses. This allowed our interpretation of the findings to be guided by patterns within the data rather than our preconceptions about which proteins or processes are of greatest interest. Moreover, we demonstrate that this novel approach can be applied to 2D gel analysis, which is unsurpassed in its ability to profile protein species but currently has few dedicated bioinformatic tools.

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JO - Journal of Proteomics

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