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Liu N.Q.,Erasmus Medical Center | Liu N.Q.,Erasmus University Rotterdam | Liu N.Q.,Netherlands Proteomics Center | Stingl C.,Erasmus University Rotterdam | And 31 more authors.
Journal of the National Cancer Institute | Year: 2014

Background: Clinical outcome of patients with triple-negative breast cancer (TNBC) is highly variable. This study aims to identify and validate a prognostic protein signature for TNBC patients to reduce unnecessary adjuvant systemic therapy. Methods: Frozen primary tumors were collected from 126 lymph node-negative and adjuvant therapy-naive TNBC patients. These samples were used for global proteome profiling in two series: an in-house training (n = 63) and a multicenter test (n = 63) set. Patients who remained free of distant metastasis for a minimum of 5 years after surgery were defined as having good prognosis. Cox regression analysis was performed to develop a prognostic signature, which was independently validated. All statistical tests were two-sided. Results: An 11-protein signature was developed in the training set (median follow-up for good-prognosis patients = 117 months) and subsequently validated in the test set (median follow-up for good-prognosis patients = 108 months) showing 89.5% sensitivity (95% confidence interval [CI] = 69.2% to 98.1%), 70.5% specificity (95% CI = 61.7% to 74.2%), 56.7% positive predictive value (95% CI = 43.8% to 62.1%), and 93.9% negative predictive value (95% CI = 82.3% to 98.9%) for poor-prognosis patients. The predicted poor-prognosis patients had higher risk to develop distant metastasis than the predicted good-prognosis patients in univariate (hazard ratio [HR] = 13.15; 95% CI = 3.03 to 57.07; P =.001) and multivariable (HR = 12.45; 95% CI = 2.67 to 58.11; P =.001) analysis. Furthermore, the predicted poor-prognosis group had statistically significantly more breast cancer-specific mortality. Using our signature as guidance, more than 60% of patients would have been exempted from unnecessary adjuvant chemotherapy compared with conventional prognostic guidelines. Conclusions: We report the first validated proteomic signature to assess the natural course of clinical TNBC. © The Author 2014. All rights reserved.


News Article | November 17, 2016
Site: www.eurekalert.org

Good cholesterol is well associated with lower cardiovascular disease risk, but just raising high-density lipoprotein (HDL) levels have produced disappointing results in recent clinical trials. A study published November 17 in Cell Metabolism may explain why: HDL actually increases the inflammatory response of immune cells called macrophages, potentially counteracting its well-established anti-inflammatory effect in various other cell types. "A main take-home message of our study is that HDL's functions are not as simple as initially thought, and appear to critically depend on the target tissue and cell type," says senior study author Marjo Donners of Maastricht University. "In the end, it is the balance between its pro- and anti-inflammatory effects that determines clinical outcome." Based on decades of research in humans and animals, HDL has gained its now well-established reputation as the "good cholesterol." High HDL levels have been associated with a lower risk of atherosclerosis--an inflammatory disease that causes plaque to build up inside of arteries. In contrast to low-density lipoprotein, which is responsible for depositing cholesterol in vessel walls, HDL removes cholesterol and transports it toward the liver for degradation. Specifically, HDL protects against atherosclerosis by inhibiting inflammation in two important vascular wall cells: endothelial cells and smooth muscle cells. However, macrophages are key immune cells contributing to the inflammation that characterizes atherosclerosis. Surprisingly, the effect of HDL on the inflammatory response in macrophages has not been clear. In the new study, Donners and first co-author Emiel van der Vorst of Maastricht University set out to address this question. Unexpectedly, they found that HDL treatment enhanced inflammation in macrophages, in contrast to its effects in other cell types. Similarly, macrophages taken from mice with elevated HDL levels showed clear signs of inflammation. This pro-inflammatory effect induced by HDL had at least one benefit: enhanced pathogen protection. Lung macrophages ingested disease-causing bacteria upon exposure to HDL. On the other hand, mice with low HDL levels were impaired at clearing these bacteria from the lungs. The results demonstrate that HDL's pro-inflammatory activity supports the proper functioning of macrophage immune responses. According to Donners, these findings suggest that patients with persistent infections or specific immune disorders might benefit from HDL-raising therapies. However, several study limitations complicate clinical interpretations. For one, the study focused on acute inflammatory responses rather than the chronic inflammatory conditions that characterize cardiovascular diseases. Moreover, the researchers did not examine macrophages specifically in atherosclerotic tissue. "Whether HDL exerts beneficial or detrimental effects on the macrophage in a complex micro-environment, such as the atherosclerotic plaque, remains to be determined," Donners says. The answer to this question may depend on disease stage and the net effect on all vascular wall cells. "For instance, in early atherosclerosis, a proper macrophage response could result in more effective scavenging and elimination of lipids and cellular debris, which may alleviate disease, whereas at later stages, such exaggerated responses may be detrimental because they destabilize the plaque," she says. "Moreover, the overt anti-inflammatory effects in other cell types should be taken into account, and it is the balance between these opposite effects of HDL that will determine clinical outcome for cardiovascular disease patients." In the end, this research could lead to the development of cell-specific therapies that exploit the benefits of HDL-targeted therapies while avoiding the side effects. "Future studies will have to evaluate the delicate balance of HDL's cell-specific effects in humans and in various pathologies to get more insights and to develop and improve therapeutic strategies," Donners says. This study was supported by grants from CARIM, the Deutsche Forschungsgemeinschaft, the Alexander von Humboldt Foundation, France "Vaincre la Mucoviscidose," the Australian Heart Foundation, the Netherlands Organisation for Scientific Research, ZonMw, the Dutch Arthritis Association, the Center for Translational Molecular Medicine project PREDICCt, the Dutch Heart Foundation, the Dutch Diabetes Research Foundation, the Dutch Kidney Foundation, and the Netherlands Heart Foundation. Cell Metabolism, van der Vorst and Theodorou et al.: "High-Density Lipoproteins Exert Pro-Inflammatory Effects on Macrophages via Passive Cholesterol Depletion and PKC-NF-kB/STAT1-IRF1 Signaling" http://www.cell.com/cell-metabolism/fulltext/S1550-4131(16)30544-7 Cell Metabolism (@Cell_Metabolism), published by Cell Press, is a monthly journal that publishes reports of novel results in metabolic biology, from molecular and cellular biology to translational studies. The journal aims to highlight work addressing the molecular mechanisms underlying physiology and homeostasis in health and disease. Visit: http://www. . To receive Cell Press media alerts, contact press@cell.com.


Liu N.Q.,Erasmus Medical Center | Liu N.Q.,Netherlands Proteomics Center | Braakman R.B.H.,Erasmus Medical Center | Braakman R.B.H.,Center for Translational Molecular Medicine | And 13 more authors.
Journal of Mammary Gland Biology and Neoplasia | Year: 2012

Mass spectrometry (MS)-based label-free proteomics offers an unbiased approach to screen biomarkers related to disease progression and therapy-resistance of breast cancer on the global scale. However, multi-step sample preparation can introduce large variation in generated data, while inappropriate statistical methods will lead to false positive hits. All these issues have hampered the identification of reliable protein markers. A workflow, which integrates reproducible and robust sample preparation and data handling methods, is highly desirable in clinical proteomics investigations. Here we describe a label-free tissue proteomics pipeline, which encompasses laser capture microdissection (LCM) followed by nanoscale liquid chromatography and high resolution MS. This pipeline routinely identifies on average ̃10,000 peptides corresponding to ̃1,800 proteins from sub-microgram amounts of protein extracted from ̃4,000 LCM breast cancer epithelial cells. Highly reproducible abundance data were generated from different technical and biological replicates. As a proof-of-principle, comparative proteome analysis was performed on estrogen receptor a positive or negative (ER+/-) samples, and commonly known differentially expressed proteins related to ER expression in breast cancer were identified. Therefore, we show that our tissue proteomics pipeline is robust and applicable for the identification of breast cancer specific protein markers. © The Author(s) 2012.


Braakman R.B.H.,Erasmus Medical Center | Braakman R.B.H.,Center for Translational Molecular Medicine | Umar A.,Erasmus Medical Center | Umar A.,Center for Translational Molecular Medicine
Current Proteomics | Year: 2013

Posttranslational modifications (PTMs) are dynamic regulators of protein function, and play important roles in diseases such as cancer. PTM analysis can be challenging, the stoichiometry of PTMs is often low, and various combinatorial modifications are possible. Currently, two major techniques are used to detect and characterize PTMs, immunoassays and mass spectrometry. Immunoassays rely on antibodies for detection of the protein of interest, and are therefore limited to targeted analysis. Mass spectrometry, on the other hand, is capable of characterizing posttranslational modifications both in targeted or non-targeted methods. Recently, new immunoassays were introduced that improve current methods, but also appear particularly promising in the analysis of PTMs. Two of these new immunoassays, proximity ligation assay and nanoscale immunoassay, are discussed in this review. In contrast to immunoassays, mass spectrometry enables characterization of a priori unknown PTM sites. A bottom-up approach, in which proteins are digested into smaller peptides, is well suited for targeted assays as well as cataloging PTMs. A top-down approach, where intact proteins are measured, is challenging but allows mapping of combinatorial PTMs. Mass spectrometry and immunoassays are therefore complementary techniques in analysis of PTMs. Advances in these methods now enable extremely sensitive detection of PTMs from very little material (immunoassays), or can fully characterize combinatorial modifications on proteins in both targeted and non-targeted ways (mass spectrometry). Recent developments in these techniques discussed in this review will therefore likely play an important role in current and future PTM analysis, particularly in the field of cancer research. © 2013 Bentham Science Publishers.

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