Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry

Lucy Jankova; Charles Chan; Caroline L. S. Fung; Xiaomin Song; Sun Y. Kwun; Mark J. Cowley; Warren Kaplan; Owen F. Dent; Elie L. Bokey; Pierre H. Chapuis; Mark S. Baker; Graham R. Robertson; Stephen J. Clarke; Mark P. Molloy

doi:10.1039/c1mb05236e

Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry

Lucy Jankova, Charles Chan, Caroline L. S. Fung, Xiaomin Song, Sun Y. Kwun, Mark J. Cowley, Warren Kaplan, Owen F. Dent, Elie L. Bokey, Pierre H. Chapuis, Mark S. Baker, Graham R. Robertson, Stephen J. Clarke, Mark P. Molloy

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Abstract

Quantitative mass spectrometry using iTRAQ was used to identify differentially expressed proteins from 16 colorectal cancer (CRC) tumours compared to patient-paired adjacent normal mucosa. Over 1400 proteins were identified and quantitated, with 118 determined as differentially expressed by >1.3-fold, with false discovery rate < 0.05. Gene Ontology analysis indicated that proteins with increased expression levels in CRC tumours include those associated with glycolysis, calcium binding, and protease inhibition. Proteins with reduced levels in CRC tumours were associated with loss of ATP production through: (i) reduced β-oxidation of fatty acids, (ii) reduced NADH production by the tricarboxylic acid cycle and (iii) decreased oxidative phosphorylation activity. Additionally, biosyntheses of glycosaminoglycans and proteoglycans were significantly reduced in tumour samples. Validation experiments using immunoblotting and immunohistochemistry (IHC) showed strong concordance with iTRAQ data suggesting that this workflow is suitable for identifying biomarker candidates. We discuss the uses and challenges of this approach to generate biomarker leads for patient prognostication.

Original language	English
Pages (from-to)	2997-3005
Number of pages	9
Journal	Molecular Biosystems
Volume	7
Issue number	11
DOIs	https://doi.org/10.1039/c1mb05236e
Publication status	Published - 2011

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Jankova, L., Chan, C., Fung, C. L. S., Song, X., Kwun, S. Y., Cowley, M. J., Kaplan, W., Dent, O. F., Bokey, E. L., Chapuis, P. H., Baker, M. S., Robertson, G. R., Clarke, S. J., & Molloy, M. P. (2011). Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry. Molecular Biosystems, 7(11), 2997-3005. https://doi.org/10.1039/c1mb05236e

@article{e975c470769c4a3f86b3b4c7774145a1,

title = "Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry",

abstract = "Quantitative mass spectrometry using iTRAQ was used to identify differentially expressed proteins from 16 colorectal cancer (CRC) tumours compared to patient-paired adjacent normal mucosa. Over 1400 proteins were identified and quantitated, with 118 determined as differentially expressed by >1.3-fold, with false discovery rate < 0.05. Gene Ontology analysis indicated that proteins with increased expression levels in CRC tumours include those associated with glycolysis, calcium binding, and protease inhibition. Proteins with reduced levels in CRC tumours were associated with loss of ATP production through: (i) reduced β-oxidation of fatty acids, (ii) reduced NADH production by the tricarboxylic acid cycle and (iii) decreased oxidative phosphorylation activity. Additionally, biosyntheses of glycosaminoglycans and proteoglycans were significantly reduced in tumour samples. Validation experiments using immunoblotting and immunohistochemistry (IHC) showed strong concordance with iTRAQ data suggesting that this workflow is suitable for identifying biomarker candidates. We discuss the uses and challenges of this approach to generate biomarker leads for patient prognostication.",

author = "Lucy Jankova and Charles Chan and Fung, {Caroline L. S.} and Xiaomin Song and Kwun, {Sun Y.} and Cowley, {Mark J.} and Warren Kaplan and Dent, {Owen F.} and Bokey, {Elie L.} and Chapuis, {Pierre H.} and Baker, {Mark S.} and Robertson, {Graham R.} and Clarke, {Stephen J.} and Molloy, {Mark P.}",

year = "2011",

doi = "10.1039/c1mb05236e",

language = "English",

volume = "7",

pages = "2997--3005",

journal = "Molecular Biosystems",

issn = "1742-2051",

publisher = "Royal Society of Chemistry",

number = "11",

}

Jankova, L, Chan, C, Fung, CLS, Song, X, Kwun, SY, Cowley, MJ, Kaplan, W, Dent, OF, Bokey, EL, Chapuis, PH, Baker, MS, Robertson, GR, Clarke, SJ & Molloy, MP 2011, 'Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry', Molecular Biosystems, vol. 7, no. 11, pp. 2997-3005. https://doi.org/10.1039/c1mb05236e

TY - JOUR

T1 - Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry

AU - Jankova, Lucy

AU - Chan, Charles

AU - Fung, Caroline L. S.

AU - Song, Xiaomin

AU - Kwun, Sun Y.

AU - Cowley, Mark J.

AU - Kaplan, Warren

AU - Dent, Owen F.

AU - Bokey, Elie L.

AU - Chapuis, Pierre H.

AU - Baker, Mark S.

AU - Robertson, Graham R.

AU - Clarke, Stephen J.

AU - Molloy, Mark P.

PY - 2011

Y1 - 2011

N2 - Quantitative mass spectrometry using iTRAQ was used to identify differentially expressed proteins from 16 colorectal cancer (CRC) tumours compared to patient-paired adjacent normal mucosa. Over 1400 proteins were identified and quantitated, with 118 determined as differentially expressed by >1.3-fold, with false discovery rate < 0.05. Gene Ontology analysis indicated that proteins with increased expression levels in CRC tumours include those associated with glycolysis, calcium binding, and protease inhibition. Proteins with reduced levels in CRC tumours were associated with loss of ATP production through: (i) reduced β-oxidation of fatty acids, (ii) reduced NADH production by the tricarboxylic acid cycle and (iii) decreased oxidative phosphorylation activity. Additionally, biosyntheses of glycosaminoglycans and proteoglycans were significantly reduced in tumour samples. Validation experiments using immunoblotting and immunohistochemistry (IHC) showed strong concordance with iTRAQ data suggesting that this workflow is suitable for identifying biomarker candidates. We discuss the uses and challenges of this approach to generate biomarker leads for patient prognostication.

AB - Quantitative mass spectrometry using iTRAQ was used to identify differentially expressed proteins from 16 colorectal cancer (CRC) tumours compared to patient-paired adjacent normal mucosa. Over 1400 proteins were identified and quantitated, with 118 determined as differentially expressed by >1.3-fold, with false discovery rate < 0.05. Gene Ontology analysis indicated that proteins with increased expression levels in CRC tumours include those associated with glycolysis, calcium binding, and protease inhibition. Proteins with reduced levels in CRC tumours were associated with loss of ATP production through: (i) reduced β-oxidation of fatty acids, (ii) reduced NADH production by the tricarboxylic acid cycle and (iii) decreased oxidative phosphorylation activity. Additionally, biosyntheses of glycosaminoglycans and proteoglycans were significantly reduced in tumour samples. Validation experiments using immunoblotting and immunohistochemistry (IHC) showed strong concordance with iTRAQ data suggesting that this workflow is suitable for identifying biomarker candidates. We discuss the uses and challenges of this approach to generate biomarker leads for patient prognostication.

UR - http://handle.uws.edu.au:8081/1959.7/557196

U2 - 10.1039/c1mb05236e

DO - 10.1039/c1mb05236e

M3 - Article

C2 - 21808808

SN - 1742-2051

VL - 7

SP - 2997

EP - 3005

JO - Molecular Biosystems

JF - Molecular Biosystems

IS - 11

ER -

Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry

Abstract

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