A novel proteogenomics approach identifying key proteins in severe COPD

Brandsma, C. A., Guryev, V., Timens, W., Postma, D. S., Bischoff, R., Yakovleva, M., Marko-Varga, G., Fehniger, T., Van Den Berge, M. & Horvatovich, P., 27-Aug-2017, In : American Journal of Respiratory and Critical Care Medicine. 195, 1 p., C74.

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  • A novel proteogenomics approach identifying key proteins in severe COPD

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Rationale COPD is influenced by many genetic and environmental factors. Genetic studies provided insights in the molecular mechanisms underlying COPD, but did not inform on protein changes. We propose that whichever factor contributes to disease, the final common pathway for disease development lies in the proteome. Therefore, we performed a combined proteome and RNA sequencing analysis comparing severe COPD and non-COPD control lung tissue. Methods Frozen lung tissue samples from 10 ex-smoking stage IV COPD patients and 10 ex-smoking non-COPD controls were used for protein and RNA extraction using urea and ammonium bicarbonate buffer and Trizol, respectively. The trypsin digested protein extract was analysed with LC-MS/MS approach using the Q-Exactive Plus (Thermo Scientific). RNA sequencing was performed with polyA-selected RNA sequencing using strand-specific quantitative NextFlex qRNA-Seq kit (Bio scientific) on Illumina HiSeq 2500 equipment with 20 million sequencing reads. We constructed patient specific protein reference databases using the RNA sequencing data and these were used to optimise peptide and protein identification. Differential gene and protein expression was assessed using linear models correcting for age, gender, age x gender interaction, and unwanted variation. FDR
Original languageEnglish
Article numberC74
Number of pages1
JournalAmerican Journal of Respiratory and Critical Care Medicine
Publication statusPublished - 27-Aug-2017
EventC74 Advances in translational COPD - Walter E. Washington Convention Center, Washington, United States
Duration: 23-May-201723-May-2017


C74 Advances in translational COPD


Washington, United States

Event: Conference


  • buffer, collagen type 14, cyclic AMP dependent protein kinase anchoring protein, endogenous compound, interleukin 6, interleukin 8, messenger RNA, peptide, protein, proteome, thrombospondin 1, thrombospondin 2, thymosin, thymosin beta4, trypsin, unclassified drug, undulin, urea, chronic obstructive lung disease, controlled study, elastic fiber, extract, female, gender, gene expression regulation, genetic analyzer, human, human tissue, liquid chromatography-mass spectrometry, lung parenchyma, major clinical study, male, mass spectrometer, muscle function, protein analysis, protein expression, proteogenomics, reference database, RNA extraction, RNA sequence, smoking, smooth muscle, statistical model

ID: 47142925