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Proteomic biomarkers for acute interstitial lung disease in gefitinib-treated Japanese lung cancer patients.

Nyberg F, Ogiwara A, Harbron CG, Kawakami T, Nagasaka K, Takami S, Wada K, Tu HK, Otsuji M, Kyono Y, Dobashi T, Komatsu Y, Kihara M, Akimoto S, Peers IS, South MC, Higenbottam T, Fukuoka M, Nakata K, Ohe Y, Kudoh S, Clausen IG, Nishimura T, Marko-Varga G, Kato H - PLoS ONE (2011)

Bottom Line: After alignment, scaling, and measurement batch adjustment, we identified 41 peptide peaks representing 29 proteins best predicting ILD.The acute phase response pathway was strongly represented (17 of 29 proteins, p = 1.0×10(-25)), suggesting a key role with potential utility as a marker for increased risk of acute ILD events.Validation by Western blotting showed correlation for identified proteins, confirming that robust results can be generated from an MS/MS platform implementing strict quality control.

View Article: PubMed Central - PubMed

Affiliation: Global Epidemiology, AstraZeneca R&D, Mölndal, Sweden. Fredrik.Nyberg@astrazeneca.com

ABSTRACT
Interstitial lung disease (ILD) events have been reported in Japanese non-small-cell lung cancer (NSCLC) patients receiving EGFR tyrosine kinase inhibitors. We investigated proteomic biomarkers for mechanistic insights and improved prediction of ILD. Blood plasma was collected from 43 gefitinib-treated NSCLC patients developing acute ILD (confirmed by blinded diagnostic review) and 123 randomly selected controls in a nested case-control study within a pharmacoepidemiological cohort study in Japan. We generated ∼7 million tandem mass spectrometry (MS/MS) measurements with extensive quality control and validation, producing one of the largest proteomic lung cancer datasets to date, incorporating rigorous study design, phenotype definition, and evaluation of sample processing. After alignment, scaling, and measurement batch adjustment, we identified 41 peptide peaks representing 29 proteins best predicting ILD. Multivariate peptide, protein, and pathway modeling achieved ILD prediction comparable to previously identified clinical variables; combining the two provided some improvement. The acute phase response pathway was strongly represented (17 of 29 proteins, p = 1.0×10(-25)), suggesting a key role with potential utility as a marker for increased risk of acute ILD events. Validation by Western blotting showed correlation for identified proteins, confirming that robust results can be generated from an MS/MS platform implementing strict quality control.

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Related in: MedlinePlus

Quality control: reproducibility of control samples and sample duplicates.(A) Reproducibility of 6 control peaks for the 3 standard quality control samples, plotted as ‘+’, in each analysis batch (peak intensity, left axis). The coefficients of variation (%, right axis) between the 3 control samples in each batch are plotted as points joined by a line. (B) Reproducibility of peptide intensities for 39 samples with duplicate analyses in different analysis batches. Partial correlation, after removing between batch differences, plotted against the average normalized intensity for each peptide. Higher intensity peptides show high reproducibility in their intensities between repeated batches.
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pone-0022062-g001: Quality control: reproducibility of control samples and sample duplicates.(A) Reproducibility of 6 control peaks for the 3 standard quality control samples, plotted as ‘+’, in each analysis batch (peak intensity, left axis). The coefficients of variation (%, right axis) between the 3 control samples in each batch are plotted as points joined by a line. (B) Reproducibility of peptide intensities for 39 samples with duplicate analyses in different analysis batches. Partial correlation, after removing between batch differences, plotted against the average normalized intensity for each peptide. Higher intensity peptides show high reproducibility in their intensities between repeated batches.

Mentions: LC-MS/MS measurements for the 181 individual baseline samples were performed in 11 batches, with 19 and 20 samples from batches 1 and 3 repeated in batches 10 and 11, respectively (Table 1), resulting in 220 discrete proteomics measurements. Four of the 11 batches initially failed the quality control criteria (coefficient of variation [CoV] >20% for any one of the six control peptides among the three within-batch control samples) on the first measurement run, but passed the criteria on repeated measurement. A quality control summary of acceptable batch runs is given in Figure 1A.


Proteomic biomarkers for acute interstitial lung disease in gefitinib-treated Japanese lung cancer patients.

Nyberg F, Ogiwara A, Harbron CG, Kawakami T, Nagasaka K, Takami S, Wada K, Tu HK, Otsuji M, Kyono Y, Dobashi T, Komatsu Y, Kihara M, Akimoto S, Peers IS, South MC, Higenbottam T, Fukuoka M, Nakata K, Ohe Y, Kudoh S, Clausen IG, Nishimura T, Marko-Varga G, Kato H - PLoS ONE (2011)

Quality control: reproducibility of control samples and sample duplicates.(A) Reproducibility of 6 control peaks for the 3 standard quality control samples, plotted as ‘+’, in each analysis batch (peak intensity, left axis). The coefficients of variation (%, right axis) between the 3 control samples in each batch are plotted as points joined by a line. (B) Reproducibility of peptide intensities for 39 samples with duplicate analyses in different analysis batches. Partial correlation, after removing between batch differences, plotted against the average normalized intensity for each peptide. Higher intensity peptides show high reproducibility in their intensities between repeated batches.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3140475&req=5

pone-0022062-g001: Quality control: reproducibility of control samples and sample duplicates.(A) Reproducibility of 6 control peaks for the 3 standard quality control samples, plotted as ‘+’, in each analysis batch (peak intensity, left axis). The coefficients of variation (%, right axis) between the 3 control samples in each batch are plotted as points joined by a line. (B) Reproducibility of peptide intensities for 39 samples with duplicate analyses in different analysis batches. Partial correlation, after removing between batch differences, plotted against the average normalized intensity for each peptide. Higher intensity peptides show high reproducibility in their intensities between repeated batches.
Mentions: LC-MS/MS measurements for the 181 individual baseline samples were performed in 11 batches, with 19 and 20 samples from batches 1 and 3 repeated in batches 10 and 11, respectively (Table 1), resulting in 220 discrete proteomics measurements. Four of the 11 batches initially failed the quality control criteria (coefficient of variation [CoV] >20% for any one of the six control peptides among the three within-batch control samples) on the first measurement run, but passed the criteria on repeated measurement. A quality control summary of acceptable batch runs is given in Figure 1A.

Bottom Line: After alignment, scaling, and measurement batch adjustment, we identified 41 peptide peaks representing 29 proteins best predicting ILD.The acute phase response pathway was strongly represented (17 of 29 proteins, p = 1.0×10(-25)), suggesting a key role with potential utility as a marker for increased risk of acute ILD events.Validation by Western blotting showed correlation for identified proteins, confirming that robust results can be generated from an MS/MS platform implementing strict quality control.

View Article: PubMed Central - PubMed

Affiliation: Global Epidemiology, AstraZeneca R&D, Mölndal, Sweden. Fredrik.Nyberg@astrazeneca.com

ABSTRACT
Interstitial lung disease (ILD) events have been reported in Japanese non-small-cell lung cancer (NSCLC) patients receiving EGFR tyrosine kinase inhibitors. We investigated proteomic biomarkers for mechanistic insights and improved prediction of ILD. Blood plasma was collected from 43 gefitinib-treated NSCLC patients developing acute ILD (confirmed by blinded diagnostic review) and 123 randomly selected controls in a nested case-control study within a pharmacoepidemiological cohort study in Japan. We generated ∼7 million tandem mass spectrometry (MS/MS) measurements with extensive quality control and validation, producing one of the largest proteomic lung cancer datasets to date, incorporating rigorous study design, phenotype definition, and evaluation of sample processing. After alignment, scaling, and measurement batch adjustment, we identified 41 peptide peaks representing 29 proteins best predicting ILD. Multivariate peptide, protein, and pathway modeling achieved ILD prediction comparable to previously identified clinical variables; combining the two provided some improvement. The acute phase response pathway was strongly represented (17 of 29 proteins, p = 1.0×10(-25)), suggesting a key role with potential utility as a marker for increased risk of acute ILD events. Validation by Western blotting showed correlation for identified proteins, confirming that robust results can be generated from an MS/MS platform implementing strict quality control.

Show MeSH
Related in: MedlinePlus