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• W2157399587 abstract "Membrane proteins constitute 20-30 % of the human genome and make up 60 % of all drug targets. They play important roles in key cellular functions such as small molecules transport, cell-cell interactions and cell signaling. Membrane proteins and proteomics have been notoriously difficult to combine. Most proteomic methods commonly used for analysis of soluble proteins cannot be used for membrane proteins, mainly due to their amphipathic nature. In this thesis, a method is described for quantitative proteomic analysis of membrane protein enriched samples. In paper I the method is applied to small cell lung cancer cell lines to elucidate Doxorubicin resistance mechanisms. We demonstrate that the microsomal preparation and iTRAQ labeling is reproducible regarding protein content and composition. The rationale using narrow range peptide isoelectric focusing separation is demonstrated by its ability to: i) lowering the complexity of the sample by two thirds while keeping a high proteome coverage (96%), ii) providing high separation efficiency and iii) allowing for peptide validation and possibly identifications of post transcriptional modifications. The work from paper I encouraged us to further explore the properties of narrow range peptide IEF as a separation strategy. We and others have shown that using IEF as the first dimension of separation is a highly suitable method when analyzing complex samples. It provides an orthogonal separation strategy to reversed phase chromatography as well as giving the opportunity to reduce false positives and false negatives generated in the database search, using the pI values of the peptides. In paper II, we wanted to explore the possibilities of using a combination of narrow range peptide IEF and reversed phase chromatography to increase the information content of a proteomic analysis. In the final two papers of this thesis, the method described in paper I is subsequently applied to clinical material. In paper III, the membrane protein fractions of benign and malignant adrenocortical tumors are compared. The mitochondrial membrane protein GRIM-19, a negative regulator of STAT3, is identified as down-regulated in the malignant tissue. The possible role of GRIM-19 down-regulation in the tumorigenesis is discussed. In paper IV, the membrane-associated protein population of alveolar macrophages isolated from Sarcoidosis patients is compared with healthy controls. Affected pathways are described and discussed. LIST OF PUBLICATIONS I. Eriksson, H.; Lengqvist, J.; Hedlund, J.; Uhlen, K.; Orre, L. M.; Bjellqvist, B.; Persson, B.; Lehtio, J.; Jakobsson, P-J., Quantitative membrane proteomics applying narrow range peptide isoelectric focusing for studies of small cell lung cancer resistance mechanisms. Proteomics 2008, 8(15):3008-18. II. Lengqvist, J.; Eriksson, H.; Gry, M.; Uhlen, K.; Bjorklund, C.; Bjellqvist, B.; Jakobsson, P-J.; Lehtio, J., Observed peptide pI and retention time shifts as a result of post-translational modifications in multidimensional separations using narrow-range IPG-IEF. Amino Acids 2010, 40(2):697-711. III. Eriksson, H.; Johansson, H.; Hoog, A., Lehtio, J.; Kjellman, M.; Jakobsson, P-J., Membrane proteomics analysis of adrenocortical tumors identifies a down-regulation of the tumor suppressor protein GRIM-19 in malignant tissue compared to benign. Manuscript IV. Silva, E*.; Eriksson, H*.; Mamede Branca, R.; Eklund, A.; Jakobsson, P-J.; Grunewald, J.; Lehtio, J.; Wheelock, A., Proteomic analysis of membraneassociated proteins in alveolar macrophages from patients with pulmonary sarcoidosis. Manuscript *Equal contribution Additional publications Maddalo, G.; Stenberg Bruzell, F.; Gotzke, H.; Toddo, S.; Bjorkholm, P.; Eriksson, H.; Chovanec, P.; Genevaux, P.; Lehtio, J.; Ilag, L. L.; Daley, D. O., A systematic analysis of native membrane protein complexes in Escherichia coli. J Proteome Res 2011, Jan 7 (epub ahead of print). Hermansson, M.; Artemenko, K.; Ossipova, E.; Eriksson, H.; Lengqvist, J.; Makrygiannakis, D.; Catrina, A. I.; Nicholas, A. P.; Klareskog, L.; Savitski, M. A.; Zubarev, R.; Jakobsson, P-J., MS analysis of rheumatoid arthritic synovial tissue identifies specific citrullination sites on fibrinogen. Proteomics Clin Appl. 2010, May;4(5):511-8. Pernemalm, M.; De Petris, L.; Eriksson, H.; Branden, E.; Koyi, H.; Kanter, L.; Lewensohn, R.; Lehtio, J., Use of narrow-range peptide IEF to improve detection of lung adenocarcinoma markers in plasma and pleural effusion. Proteomics 2009, Jul;9(13):3414-24. Silva, E.; Bourin, S.; Sabounchi-Schutt, F.; Laurin, Y.; Barker, E.; Newman, L.; Eriksson, H.; Eklund, A.; Grunewald, J., A quantitative proteomic analysis of soluble bronchoalveolar fluid proteins from patients with sarcoidosis and chronic beryllium disease. Sarcoidosis Vasc Diffuse Lung Dis 2007, Mar;24(1):24-32." @default.
• W2157399587 created "2016-06-24" @default.
• W2157399587 creator A5084535555 @default.
• W2157399587 date "2011-03-11" @default.
• W2157399587 modified "2023-09-27" @default.
• W2157399587 title "MEMBRANE PROTEINS AND PROTEOMICS - UN AMOUR POSSIBLE?" @default.
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