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| 2. |
- Borrebaeck, Carl
(författare)
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Viewpoints in Clinical Proteomics - when will proteomics deliver clinically useful information?
- 2012
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Ingår i: Proteomics Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 6:7-8, s. 343-345
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Tidskriftsartikel (refereegranskat)abstract
- Proteomics has not delivered biomarkers of clinical value, despite massive efforts. The technologies that are emerging today have, however, the power to reach deep into proteomes and to identify patterns associated with different diseases. The study design is then crucial and sample quality, bioinformatic approaches, pre-validation, using independent patient cohort, need to attract increased attention before proteomics will contribute to the needs of personalized medicine.
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| 3. |
- Carlsson, Anders, et al.
(författare)
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Plasma proteome profiling reveals biomarker patterns associated with prognosis and therapy selection in glioblastoma multiforme patients
- 2010
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Ingår i: Proteomics Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 4:6-7, s. 591-602
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Glioblastoma multiforme (GBM) is a frequent and aggressive type of primary brain tumor with a heterogeneous origin. GBM is highly therapy resistant and carries a dismal prognosis for the patient. The purpose of this discovery study was to define candidate plasma biomarker signatures for improved classification and novel means for selecting patients for refined individualized therapy. Experimental design: Here, we have for the first time investigated the applicability of large-scale recombinant antibody-based microarrays, targeting mainly immunoregulatory analytes, for sensitive and selective plasma protein profiling of GBM patients undergoing immunotherapy with autologous IFN-gamma transfected glioma cells Results: This proof-of-concept study showed that candidate plasma protein signatures associated with GBM were outlined that could be used for GBM classification, monitoring the effects of the immunotherapy as well as for stratifying patients according to the beneficial effect of the adopted immunotherapy Further, central key cytokines that could be utilized for optimization and/or refinement of the immunotherapeutic regime were indicated. Conclusions and clinical relevance: Candidate plasma proteins signatures associated with GBM was outlined, that could be used for GBM classification and for pre-operatively stratifying patients according to the beneficial effect of the adopted immunotherapy.
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| 4. |
- Dexlin Mellby, Linda, et al.
(författare)
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Tissue proteome profiling of preeclamptic placenta using recombinant antibody microarrays
- 2010
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Ingår i: Proteomics Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 4:10-11, s. 794-807
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: preeclampsia (PE) is a severe, multi-system pregnancy disorder of yet unknown cause, missing means of treatment, and our fundamental understanding of the disease is still impaired. The purpose of this discovery study was to define candidate placenta tissue protein biomarker signatures to further decipher the molecular features of PE.EXPERIMENTAL DESIGN: we used recombinant antibody microarrays for multiplexed protein expression profiling of preeclamptic placenta tissue (n=25) versus normal placenta (n=11) targeting mainly immunoregulatory water-soluble proteins and membrane proteins. Furthermore, the three known subgroups of PE were profiled, including women with early onset preeclampsia and late onset preeclampsia, as well as women with PE and bilateral notching and intrauterine growth restrictions.RESULTS: the data showed that the first generation of candidate PE-associated placenta tissue protein signatures were delineated, indicating that PE (receiver operating characteristics (ROC) AUC value of 0.83) and the subgroups thereof (ROC AUC values ≤ 0.91) could be distinguished. Notably, the data implied that all subgroups, but preeclampsia with bilateral notching and IUGR, could be further classified into novel subsets (ROC AUC values of 1.0) displaying different inflammatory signatures.CONCLUSIONS AND CLINICAL RELEVANCE: we have taken one step further toward de-convoluting the complex features of PE at the molecular level using affinity proteomics.
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| 5. |
- Hermansson, Monika, et al.
(författare)
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MS analysis of rheumatoid arthritic synovial tissue identifies specific citrullination sites on fibrinogen.
- 2010
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Ingår i: Proteomics - Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 4:5, s. 511-518
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Tidskriftsartikel (refereegranskat)abstract
- Purpose Citrullination is a post-translational modification of arginine residues to citrulline catalyzed by peptidyl arginine deiminases. Induced expression of citrullinated proteins are frequently detected in various inflammatory states including arthritis; however, direct detection of citrullination in arthritic samples has not been successfully performed in the past. Experimental design Citrullination of human fibrinogen, a candidate autoantigen in arthritis, was studied. Accurate identification of citrullinated fibrinogen peptides from rheumatoid arthritis synovial tissue specimens was performed using accurate mass and retention time analysis. Results A peptide with the sequence ESSSHHPGIAEFPSRGK corresponding to amino acids 559-575 of fibrinogen a-chain was identified to be citrullinated with an occupancy rate between 1.4 and 2.5%. Citrullination of the peptide KREEAPSLRPAPPPISGGGYRARPAK corresponding to amino acids 52-77 of the fibrinogen beta-chain was identified with an occupancy rate of 1.2%. Conclusions and clinical relevance We report a proof of principle study for the identification of citrullinated proteins and within them, identification of citrullination sites and quantification of their occupancies in synovial tissue from rheumatoid arthritis patients using high-resolution MS. Detailed studies on which molecules are citrullinated in arthritis can provide information about their role in immune regulation and serve as novel biomarkers and potentially even as therapeutic targets.
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| 6. |
- Hjelm, Barbara, et al.
(författare)
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High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer
- 2011
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Ingår i: Proteomics Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 5:11-12, s. 624-635
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: In this study, we investigated the prognostic impact of human RBM3 expression in colorectal cancer using tissue microarray-based immunohistochemical analysis. Experimental design: One polyclonal antibody and four monoclonal anti-RBM3 antibodies were generated and epitope mapped using two different methods. Bacterial display revealed five distinct epitopes for the polydonal antibody, while the four mouse monoclonal antibodies were found to bind to three of the five epitopes. A peptide suspension bead array assay confirmed the five epitopes of the polydonal antibody, while only one of the monoclonal antibodies could be mapped using this approach. Antibody specificity was confirmed by Western blotting and immunohistochemistry, including siRNA-mediated knock-down. Two of the antibodies (polydonal and monoclonal) were subsequently used to analyze RBM3 expression in tumor samples from two independent colorectal cancer cohorts, one consecutive cohort (n = 270) and one prospectively collected cohort of patients with cancer of the sigmoid colon (n = 305). RBM3-expression was detected, with high correlation between both antibodies (R = 0.81, p < 0.001). Results: In both cohorts, tumors with high nuclear RBM3 staining had significantly prolonged the overall survival. This was also confirmed in multivariate analysis, adjusted for established prognostic factors. Conclusion and clinical relevance: These data demonstrate that high tumor-specific nuclear expression of RBM3 is an independent predictor of good prognosis in colorectal cancer.
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| 7. |
- Jia, Min, et al.
(författare)
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Proteome profiling of immortalization-to-senescence transition of human breast epithelial cells identified MAP2K3 as a senescence-promoting protein which is downregulated in human breast cancer
- 2010
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Ingår i: PROTEOMICS - Clinical Applications. - : Wiley. - 1862-8346 .- 1862-8354. ; 4:10-11, s. 816-828
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Immortalization is one of the first changes in cells undergoing carcinogenic transformation. Proteome profiling of the immortalization-senescence transition is expected to provide insights into the molecular mechanisms of early tumorigenesis. Experimental design: 2-DE and MALDI-MS were used to identify proteins in primary human breast epithelial cells, relevant to the immortalization-senescence transition. Cell and molecular biology and immunohistochemistry were used to validate involvement of mitogen-activated protein kinase kinase 3 (MAP2K3) in the immortalization-senescence transition. Results: We identified 71 proteins whose expression changed upon induction of senescence. The identified proteins include regulators of cell growth, death, cell assembly and organization. Analysis of the network formed by the identified proteins suggested that the immortalization-to-senescence transition could affect regulators of the cell cycle, protein synthesis, transport, post-translational modifications, DNA recombination and repair, and lipid and amino acid metabolism. We observed that MAP2K3 was downregulated in immortal human breast epithelial cells and that upregulation of MAP2K3 expression promoted cell senescence. Decreased expression of MAP2K3 was observed in human breast infiltrating ductal carcinomas, as compared to non-cancerous human breast tissues. Conclusion and clinical relevance: We described a proteome profile of the immortalization-to-senescence transition for human breast epithelial cells, and identified MAP2K3 as a protein that promotes senescence in these cells.
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| 8. |
- Kristensson, Malin, et al.
(författare)
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Design of recombinant antibody microarrays for urinary proteomics.
- 2012
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Ingår i: Proteomics Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 6:5-6, s. 291-296
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: Urinary proteomics has become a key discipline within clinical proteomics for noninvasive diagnosis and monitoring of disease, and biomarker discovery. In order to decipher complex proteomes, high demands will, however, be placed upon the methodology applied. The purpose of this study was to develop a recombinant antibody microarray platform for urinary proteomics. EXPERIMENTAL DESIGN: We adopted our previously in-house developed recombinant antibody microarray set-up and redesigned the platform for urinary proteomics. In this process, the key antibody array assay parameters, such as sample handling, sample labeling protocol, and assay conditions, etc, reflecting the unique properties of urine as sample format, were addressed and reoptimized in a step-by-step procedure. RESULTS: In this proof-of-concept study, we have designed the first generation of a recombinant antibody microarray technology platform for urinary proteomics. The results showed that multiplexed, sensitive (pg/mL range), and reproducible urine protein expression profiling could be performed targeting directly labeled, nonfractionated urine. CONCLUSION AND CLINICAL RELEVANCE: We have demonstrated that crude, directly labeled urine samples could be profiled in a rapid, reproducible, sensitive, and multiplexed manner after minimal sample prehandling. These findings could potentially pave the way for enhanced urinary proteomics and understanding of renal physiology with implications in both health and disease.
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| 9. |
- Ljunggren, Stefan, et al.
(författare)
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ApoA-I mutations, L202P and K131del, in HDL from heterozygotes with low HDL-C
- 2014
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Ingår i: PROTEOMICS - Clinical Applications. - : Wiley-Blackwell. - 1862-8346 .- 1862-8354. ; 8:3-4, s. 241-250
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: Mutations in apolipoprotein A-I (apoA-I) may affect plasma high-density lipoprotein (HDL) cholesterol levels and the risk for cardiovascular disease but little is known about the presence and effects of circulating apoA-I variants. This study investigates whether the apoA-I mutations, apoA-I(L202P) and apoA-I(K131del) , are present on plasma HDL particles derived from heterozygote carriers and whether this is associated to changes in HDL protein composition.EXPERIMENTAL DESIGN: Plasma HDL of heterozygotes for either apoA-I(L202P) or apoA-I(K131del) and family controls was isolated using ultracentrifugation. HDL proteins were separated by 2DE and analyzed by MS.RESULTS: ApoA-I peptides containing apoA-I(L202P) or apoA-I(K131del) were identified in HDL from heterozygotes. The apoA-I(L202P) mutant peptide was less abundant than wild-type peptide while the apoA-I(K131del) mutant peptide was more abundant than wild-type peptide in the heterozygotes. Two-dimensional gel electrophoresis analyses indicated that, compared to controls, HDL in apoA-I(L202P) carriers contained less apoE and more zinc-α-2-glycoprotein while HDL from the apoA-I(K131del) heterozygotes contained more alpha-1-antitrypsin and transthyretin.CONCLUSIONS AND CLINICAL RELEVANCE: Both apoA-I(L202P) and apoA-I(K131del) were identified in HDL. In heterozygotes, these mutations have markedly differential effects on the concentration of wild-type apoA-I in the circulation, as well as the HDL proteome, both of which might affect the clinical phenotype encountered in the heterozygous carriers.
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| 10. |
- Lomnytska, Marta I, et al.
(författare)
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Diagnostic protein marker patterns in squamous cervicalcancer
- 2010
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Ingår i: Proteomics - Clinical Applications. - Weinheim : WILEY-VCH Verlag GmbH & Co. KGaA. - 1862-8346 .- 1862-8354. ; 4:1, s. 17-31
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Cervical cancer is the second most prevalent malignancy of women. Our aim was toidentify additional marker protein patterns for objective diagnosis of squamous cervical cancer(SCC).Experimental design: Collected tissue biopsies of SCC, squamous vaginal cancer (SVC), normalcervical and vaginal mucosa were subjected to 2-DE, SameSpot analysis, MALDI-TOF-MSprotein identification, and analysis of the expression of selected proteins by immunohistochemistry.Results: In 148 protein spots selected by the difference in expression 99 proteins were identified.A differential protein pattern for SCC was, e.g. over-expressed (OE) eukaryotic translationinitiation factor 3-2b, neutrophil cytosolic factor 2, annexin A6 (ANXA6), for SVC it was OEcathepsin D, g-catenin, RAB2A, for both cancers it was OE apolipoprotein E, tropomyosin 3,HSPA8, and underexpressed cytokeratin 13, osteoglycin. In SCC nuclear expression ofneutrophil cytosolic factor 2, PRDX2, HSP27 (nine of ten cases), ANXA6 (nine of ten cases) wasobserved while tropomyosin 4 was expressed only in two of ten cases. There was 81.1% (43/53)agreement between the expression of protein spots and the immune expression of proteins(www.proteinatlas.org).Conclusions and clinical relevance: SCC is characterized by specific tissue marker proteinpatterns that allow objective detection of the disease. They can become a basis for objectiveautomated cytology-based screening and improve current diagnostics of SCC.
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