Quantitative mass spectrometry for colorectal cancer proteomics

Martínez‐Aguilar, Juan; Chik, Jenny H. L.; Nicholson, Judith; Semaan, Crystal; McKay, Matthew J.; Molloy, Mark P.

doi:10.1002/prca.201200080

Cited by 26 publications

(17 citation statements)

References 96 publications

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“…Several previous proteomics studies have been carried out using specimens from patients with CRC (reviewed in [7]), however, none have examined the molecular differences in tumor tissues from patients with Stage III who achieved a good outcome and those who suffered distant recurrence, or assessed the differences separately in IIIB and IIIC subgroups. In this study, we used TMT-based MS to investigate distant recurrence-associated DEPs in patients with Stage IIIB and IIIC CRC.…”

Section: Discussionmentioning

confidence: 99%

Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer

Gao

Chen

et al. 2016

Oncotarget

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Surgical resection supplemented with adjuvant chemotherapy is the current preferred treatment for Stage III colorectal cancer (CRC). However, as many as 48% of patients who undergo curative resection eventually suffer from incurable distant recurrence. To investigate the molecular mechanisms involved in Stage III CRC post-surgical distant recurrence, we identified a total of 146 differentially expressed proteins (DEPs) associated with distant recurrence in Stage III CRC using TMT-based quantitative mass spectrometry. Among these DEPs, the altered expressions of R-Ras and Transgelin were then validated in 192 individual specimens using immunohistochemistry (IHC). Furthermore, Kaplan-Meier analysis revealed that the levels of R-Ras and Transgelin were significantly associated with 5-year overall survival (OS) and disease-free survival (DFS), and multivariate Cox-regression analyses revealed that R-Ras and Transgelin were independent prognostic factors for OS and DFS, respectively. In conclusion, this study identified potential biochemical players involved in distant recurrence and indicates that R-Ras and Transgelin are potential post-surgical prognostic biomarkers for Stage III CRC. This proteomics data have been submitted to Proteome Xchange under accession number PXD002903.

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Section: Discussionmentioning

confidence: 99%

Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer

Gao

Chen

et al. 2016

Oncotarget

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show abstract

“…This section describes the data sources and additional data processing steps applied in this study. An attempt was made to locate all currently available proteomic studies for clinical tissue on CRC including, among others, those listed in the "Tissue" and "Tissue subproteomes" sections of the review paper by de Wit et al (2013) and in Supporting Table 3 ("Clinical Samples") of the review paper by Martínez-Aguilar et al (2013). To make the comparisons more robust, only datasets with at least 30 proteins in each of the up-and down-regulated groups were considered; however, all datasets from a given 5/38 study were included if at least one of the datasets met this criterion.…”

Section: Data Sourcesmentioning

confidence: 99%

Proteomic indicators of oxidation and hydration state in colorectal cancer

Dick¹

2016

Preprint

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New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer (CRC). Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (Z C ) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue (n H 2 O ) is computed by writing the overall formation reactions of proteins from basis species. Using reported results from clinical proteomic studies and microbial community profiling, many datasets exhibit higher mean Z C or n H 2 O of proteins in carcinoma or adenoma compared to normal tissue. Microbial protein compositions have lower Z C in bacteria enriched in fecal samples from cancer patients. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H 2 O and fugacity of O 2 that reflect the compositional differences. The compositional analysis suggests that a systematic shift in chemical composition is an essential feature of the cancer proteome, and the thermodynamic descriptions show that the observed proteomic transformations could be promoted by microenvironments shifted toward more oxidizing conditions and increased hydration levels.

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“…This section describes the data sources and additional data processing steps applied in this study. An attempt was made to locate all currently available proteomic studies for clinical tissue on CRC including, among others, those listed in the "Tissue" and "Tissue subproteomes" sections of the review paper by de Wit et al (2013) and in Supporting Table 3 ("Clinical Samples") of the review paper by Martínez-Aguilar et al (2013). To make the comparisons more robust, only datasets with at least 30 proteins in each of the up-and down-regulated groups were considered; however, all datasets from a given study were included if at least one of the datasets met this criterion.…”

Section: Data Sourcesmentioning

confidence: 99%

Peer Review #1 of "Proteomic indicators of oxidation and hydration state in colorectal cancer (v0.1)"

2016

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New integrative approaches are needed to harness the potential of rapidly growing datasets of protein expression and microbial community composition in colorectal cancer. Chemical and thermodynamic models offer theoretical tools to describe populations of biomacromolecules and their relative potential for formation in different microenvironmental conditions. The average oxidation state of carbon (Z C) can be calculated as an elemental ratio from the chemical formulas of proteins, and water demand per residue (nH 2 O) is computed by writing the overall formation reactions of proteins from basis species. Using results reported in proteomic studies of clinical samples, many datasets exhibit higher mean Z C or nH 2 O of proteins in carcinoma or adenoma compared to normal tissue. In contrast, average protein compositions in bacterial genomes often have lower Z C for bacteria enriched in fecal samples from cancer patients compared to healthy donors. In thermodynamic calculations, the potential for formation of the cancer-related proteins is energetically favored by changes in the chemical activity of H 2 O and fugacity of O 2 that reflect the compositional differences. The compositional analysis suggests that a systematic change in chemical composition is an essential feature of cancer proteomes, and the thermodynamic descriptions show that the observed proteomic transformations in host tissue could be promoted by relatively high microenvironmental oxidation and hydration states.

show abstract

Quantitative mass spectrometry for colorectal cancer proteomics

Cited by 26 publications

References 96 publications

Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer

Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer

Proteomic indicators of oxidation and hydration state in colorectal cancer

Peer Review #1 of "Proteomic indicators of oxidation and hydration state in colorectal cancer (v0.1)"

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