TY  - JOUR
AB  - Deltamethrin (DM) is a widely used pyrethroid pesticide associated with childhood neurodevelopmental disorders. However, the specific impact of DM exposure during distinct early life stages remains unclear. Here, zebrafish embryos were exposed to DM at different stages: before (10-16 hpf), at the onset of (16-24 hpf), at the peak of (24-36 hpf) hypothalamic neurogenesis, and continuously from 10 to 120 hpf (subchronic exposure), using different dosages (1, 100, and 250 nM). Exposure to middle/high-dose DM at 24-36 and 10-120 hpf significantly reduced zebrafish locomotor activities and increased apoptotic cells in the spinal cord. As a pivotal factor in central nervous system disorder progression, altered lipid metabolism was investigated using nontargeted lipidomic analysis. DM exposure at 10-16 and 24-36 hpf led to the most significant lipidome reprogramming. Despite exhibiting a dose-dependent trend, even low-dose DM changed the lipidome. Cer 40:2;2 and PG 44:12 showed potential in identifying DM exposure effects. Significant changes in sphingolipid, cardiolipin, phosphatidylglycerol, and glycerolipid pathways were linked to DM-induced developmental neurotoxicity, indicating impaired membrane function, mitochondrial damage, and disrupted energy metabolism. Our study sheds new light on assessing early neurodevelopmental disturbances and identifying intervention targets, emphasizing sensitivity to DM during the critical early phase of neurodevelopment.
AU  - Gao, L.*
AU  - Hao, J.*
AU  - Hua, Z.*
AU  - Zeng, C.*
AU  - Li, J.*
AU  - Zeng, J.
C1  - 73979
C2  - 57286
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
TI  - Lipidomics atlas tracks alterations associated with deltamethrin-induced developmental neurotoxicity in embryonic zebrafish.
JO  - J. Proteome Res.
PB  - Amer Chemical Soc
PY  - 2025
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Advancing MS-based proteomics toward clinical applications evolves around developing standardized start-to-finish and fit-for-purpose workflows for clinical specimens. Steps along the method design involve the determination and optimization of several bioanalytical parameters such as selectivity, sensitivity, accuracy, and precision. In a joint effort, eight proteomics laboratories belonging to the MSCoreSys initiative including the CLINSPECT-M, MSTARS, DIASyM, and SMART-CARE consortia performed a longitudinal round-robin study to assess the analysis performance of plasma and serum as clinically relevant samples. A variety of LC-MS/MS setups including mass spectrometer models from ThermoFisher and Bruker as well as LC systems from ThermoFisher, Evosep, and Waters Corporation were used in this study. As key performance indicators, sensitivity, precision, and reproducibility were monitored over time. Protein identifications range between 300 and 400 IDs across different state-of-the-art MS instruments, with timsTOF Pro, Orbitrap Exploris 480, and Q Exactive HF-X being among the top performers. Overall, 71 proteins are reproducibly detectable in all setups in both serum and plasma samples, and 22 of these proteins are FDA-approved biomarkers, which are reproducibly quantified (CV < 20% with label-free quantification). In total, the round-robin study highlights a promising baseline for bringing MS-based measurements of serum and plasma samples closer to clinical utility.
AU  - Kardell, O.
AU  - Gronauer, T.F.
AU  - von Toerne, C.
AU  - Merl-Pham, J.
AU  - König, A.-C.
AU  - Barth, T.K.*
AU  - Mergner, J.*
AU  - Ludwig, C.*
AU  - Tüshaus, J.*
AU  - Giesbertz, P.*
AU  - Breimann, S.*
AU  - Schweizer, L.*
AU  - Müller, T.*
AU  - Kliewer, G.*
AU  - Distler, U.*
AU  - Gomez-Zepeda, D.*
AU  - Popp, O.*
AU  - Qin, D.*
AU  - Teupser, D.*
AU  - Cox, J.*
AU  - Imhof, A.*
AU  - Küster, B.*
AU  - Lichtenthaler, S.F.*
AU  - Krijgsveld, J.*
AU  - Tenzer, S.*
AU  - Mertins, P.*
AU  - Coscia, F.*
AU  - Hauck, S.M.
C1  - 73315
C2  - 57009
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 1017-1029
TI  - Multicenter longitudinal quality assessment of MS-based proteomics in plasma and serum.
JO  - J. Proteome Res.
VL  - 24
IS  - 3
PB  - Amer Chemical Soc
PY  - 2025
SN  - 1535-3893
ER  - 

TY  - JOUR
AU  - Kardell, O.
AU  - Gronauer, T.F.
AU  - von Toerne, C.
AU  - Merl-Pham, J.
AU  - König, A.-C.
AU  - Barth, T.K.*
AU  - Mergner, J.*
AU  - Ludwig, C.*
AU  - Tüshaus, J.*
AU  - Giesbertz, P.*
AU  - Breimann, S.*
AU  - Schweizer, L.*
AU  - Müller, T.*
AU  - Kliewer, G.*
AU  - Distler, U.*
AU  - Aljakouch, K.*
AU  - Gomez‐Zepeda, D.*
AU  - Popp, O.*
AU  - Qin, D.*
AU  - Teupser, D.*
AU  - Cox, J.*
AU  - Imhof, A.*
AU  - Küster, B.*
AU  - Lichtenthaler, S.F.*
AU  - Krijgsveld, J.*
AU  - Tenzer, S.*
AU  - Mertins, P.*
AU  - Coscia, F.*
AU  - Hauck, S.M.
C1  - 75261
C2  - 57880
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 4862–4863
TI  - Correction to “Multicenter longitudinal quality assessment of MS-based proteomics in plasma and serum”.
JO  - J. Proteome Res.
VL  - 24
IS  - 9
PB  - Amer Chemical Soc
PY  - 2025
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Orbitrap (OT)-based mass spectrometer platforms are a gold standard in high-resolution mass spectrometry, where their primary disadvantage is slower-scanning speed in comparison to time-of-flight or linear ion trap mass analyzers. In this study, we utilize long OT transients to extend the precursor dynamic range by modifying the selected ion monitoring method to multiplex several precursor m/z ranges into a single scan, which we call "multiple accumulation precursor mass spectrometry". Our approach requires no software or hardware modifications and hides the additional ion accumulation steps during the time it takes to make other Orbitrap measurements, producing precursor spectra with nearly 2× dynamic range and essentially no consequences. We collected data using both data-dependent acquisition (DDA) and data-independent acquisition (DIA) methods to evaluate a range of approaches. With DDA, MAP-MS precursor quantification improves with higher quality measurements. At the same time, DIA detection is enhanced by up to 11% when combining precursor and tandem mass spectra for peptide detection.
AU  - Phlairaharn, T.*
AU  - Shannon, A.E.*
AU  - Zeng, X.*
AU  - Truong, D.J.J.
AU  - Schoof, E.M.*
AU  - Ye, Z.*
AU  - Searle, B.C.*
C1  - 75559
C2  - 58247
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 5116–5126
TI  - Improving proteomic dynamic range with Multiple Accumulation Precursor Mass Spectrometry. 
JO  - J. Proteome Res.
VL  - 24
IS  - 10
PB  - Amer Chemical Soc
PY  - 2025
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors. As representatives of HUPO's Human Plasma Proteome Project (HPPP), we present our 2024 survey of the current progress in our community, including the latest build of the Human Plasma Proteome PeptideAtlas that now comprises 4608 proteins detected in 113 data sets. We then discuss the updates of established proteomics methods, emerging technologies, and investigations of proteoforms, protein networks, extracellualr vesicles, circulating antibodies and microsamples. Finally, we provide a prospective view of using the current and emerging proteomics tools in studies of circulating proteins.
AU  - Geyer, P.E.*
AU  - Hornburg, D.*
AU  - Pernemalm, M.*
AU  - Hauck, S.M.
AU  - Palaniappan, K.K.*
AU  - Albrecht, V.*
AU  - Dagley, L.F.*
AU  - Moritz, R.L.*
AU  - Yu, X.*
AU  - Edfors, F.*
AU  - Vandenbrouck, Y.*
AU  - Mueller-Reif, J.B.*
AU  - Sun, Z.*
AU  - Brun, V.*
AU  - Ahadi, S.*
AU  - Omenn, G.S.*
AU  - Deutsch, E.W.*
AU  - Schwenk, J.M.*
C1  - 72211
C2  - 56475
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 5279-5295
TI  - The circulating proteome─technological developments, current challenges, and future trends.
JO  - J. Proteome Res.
VL  - 23
IS  - 12
PB  - Amer Chemical Soc
PY  - 2024
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Parkinson's disease (PD) progresses with the loss of dopaminergic neurons in the substantia nigra pars compacta region of the brain. The superior mechanisms and the cause of this specific localized neurodegeneration is currently unknown. However, experimental evidence indicates a link between PD progression and reactive oxygen species with imbalanced metal homeostasis. Wild-type Caenorhabditis elegans exposed to redox-active metals was used as the model organism to study cellular response to imbalanced metal homeostasis linked to neurodegenerative diseases. Using modern hyphenated techniques such as capillary electrophoresis coupled to inductively coupled plasma mass spectrometry and ultrahigh-performance liquid chromatography mass spectrometry, alterations in the lipidome and metallome were determined in vivo. In contrast to iron, most of the absorbed zinc and manganese were loosely bound. We observed changes in the phospholipid composition for acute iron and manganese exposures, as well as chronic zinc exposure. Furthermore, we focused on the mitochondrial membrane alteration due to its importance in neuronal function. However, significant changes in the inner mitochondrial membrane by determination of cardiolipin species could only be observed for acute iron exposure. These results indicate different intracellular sites of local ROS generation, depending on the redox active metal. Our study combines metallomic and lipidomic alterations as the cause and consequence to enlighten intracellular mechanisms in vivo, associated with PD progression. The mass spectrometry raw data have been deposited to the MassIVE database (https://massive.ucsd.edu) with the identifier MSV000090796 and 10.25345/C51J97C8F.
AU  - Blume, B.
AU  - Schwantes, V.*
AU  - Witting, M.
AU  - Hayen, H.*
AU  - Schmitt-Kopplin, P.
AU  - Helmer, P.O.*
AU  - Michalke, B.
C1  - 67117
C2  - 53558
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 837–850
TI  - Lipidomic and metallomic alteration of Caenorhabditis elegans after acute and chronic manganese, iron and zinc exposure with link to neurodegenerative disorders. 
JO  - J. Proteome Res.
VL  - 22
IS  - 3
PB  - Amer Chemical Soc
PY  - 2023
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography-mass spectrometry (LC-MS) setups. With the aim to benchmark and improve the current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium, we performed two consecutive round-robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six study partners were provided with two clinically relevant sample matrices: plasma and cerebrospinal fluid (CSF). In the first round, each laboratory applied their current best practice protocol for the respective matrix. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements.
AU  - Kardell, O.
AU  - von Toerne, C.
AU  - Merl-Pham, J.
AU  - König, A.-C.
AU  - Blindert, M.
AU  - Barth, T.K.*
AU  - Mergner, J.*
AU  - Ludwig, C.*
AU  - Tüshaus, J.*
AU  - Eckert, S.*
AU  - Müller, S.A.*
AU  - Breimann, S.*
AU  - Giesbertz, P.*
AU  - Bernhardt, A.M.J.*
AU  - Schweizer, L.*
AU  - Albrecht, V.*
AU  - Teupser, D.*
AU  - Imhof, A.*
AU  - Kuster, B.*
AU  - Lichtenthaler, S.F.*
AU  - Mann, M.*
AU  - Cox, J.*
AU  - Hauck, S.M.
C1  - 68899
C2  - 53751
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 117-129
TI  - Multicenter collaborative study to optimize mass spectrometry workflows of clinical specimens.
JO  - J. Proteome Res.
VL  - 23
IS  - 1
PB  - Amer Chemical Soc
PY  - 2023
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The plasma proteome is the ultimate target for biomarker discovery. It stores an endless amount of information on the pathophysiological status of a living organism, which is, however, still difficult to comprehensively access. The high complexity of the plasma proteome can be addressed by either a system-wide and unbiased tool such as mass spectrometry (LC-MS/MS) or a highly sensitive targeted immunoassay such as the proximity extension assay (PEA). To address relevant differences and important shared characteristics, we tested the performance of LC-MS/MS in the data-dependent and data-independent acquisition modes and Olink PEA to measure circulating plasma proteins in 173 human plasma samples from a Southern German population-based cohort. We demonstrated the measurement of more than 300 proteins with both LC-MS/MS approaches applied, mainly including high-abundance plasma proteins. By the use of the PEA technology, we measured 728 plasma proteins, covering a broad dynamic range with high sensitivity down to pg/mL concentrations. Then, we quantified 35 overlapping proteins with all three analytical platforms, verifying the reproducibility of data distributions, measurement correlation, and gender-based differential expression. Our work highlights the limitations and the advantages of both targeted and untargeted approaches and proves their complementary strengths. We demonstrated a significant gain in proteome coverage depth and subsequent biological insight by a combination of platforms - a promising approach for future biomarker and mechanistic studies.
AU  - Petrera, A.
AU  - von Toerne, C.
AU  - Behler, J.
AU  - Huth, C.
AU  - Thorand, B.
AU  - Hilgendorff, A.
AU  - Hauck, S.M.
C1  - 60833
C2  - 49246
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 751-762
TI  - Multiplatform approach for plasma proteomics: Complementarity of olink proximity extension assay technology to mass spectrometry-based protein profiling.
JO  - J. Proteome Res.
VL  - 20
IS  - 1
PB  - Amer Chemical Soc
PY  - 2021
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Trypsin is one of the most important and widely used proteolytic enzymes in mass spectrometry (MS)-based proteomic research. It exclusively cleaves peptide bonds at the C-terminus of lysine and arginine. However, the cleavage is also affected by several factors, including specific surrounding amino acids, resulting in frequent incomplete proteolysis and subsequent issues in peptide identification and quantification. The accurate annotations on missed cleavages are crucial to database searching in MS analysis. Here, we present deep-learning predicting missed cleavages (dpMC), a novel algorithm for the prediction of missed trypsin cleavage sites. This algorithm provides a very high accuracy for predicting missed cleavages with area under the curves (AUCs) of cross-validation and holdout testing above 0.99, along with the mean F1 score and the Matthews correlation coefficient (MCC) of 0.9677 and 0.9349, respectively. We tested our algorithm on data sets from different species and different experimental conditions, and its performance outperforms other currently available prediction methods. In addition, the method also provides a better insight into the detailed rules of trypsin cleavages coupled with propensity and motif analysis. Moreover, our method can be integrated into database searching in the MS analysis to identify and quantify mass spectra effectively and efficiently.
AU  - Sun, B.*
AU  - Smialowski, P.
AU  - Straub, T.*
AU  - Imhof, A.*
C1  - 62333
C2  - 50795
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 3749–3757
TI  - Investigation and highly accurate prediction of missed tryptic cleavages by deep learning.
JO  - J. Proteome Res.
VL  - 20
IS  - 7
PB  - Amer Chemical Soc
PY  - 2021
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Large-scale population screenings are not feasible by applying laborious oral glucose tolerance tests, but using fasting blood glucose (FPG) and glycated hemoglobin (HbA1c), a considerable number of diagnoses are missed. A novel marker is urgently needed to improve the diagnostic accuracy of broad-scale diabetes screening in easy-to-collect blood samples. In this study, by applying a novel knowledge-based, multistage discovery and validation strategy, we scaled down from 108 diabetes-associated metabolites to a diagnostic metabolite triplet (Met-T), namely hexose, 2-hydroxybutyric/2-hydroxyisobutyric acid, and phenylalanine. Met-T showed in two independent cohorts, each comprising healthy controls, prediabetic, and diabetic individuals, distinctly higher diagnostic sensitivities for diabetes screening than FPG alone (>79.6 vs <68%). Missed diagnoses decreased from >32% using fasting plasma glucose down to <20.4%. Combining Met-T and fasting plasma glucose further improved the diagnostic accuracy. Additionally, a positive association of Met-T with future diabetes risk was found (odds ratio: 1.41; p = 1.03 × 10-6). The results reveal that missed prediabetes and diabetes diagnoses can be markedly reduced by applying Met-T alone or in combination with FPG and it opens perspectives for higher diagnostic accuracy in broad-scale diabetes-screening approaches using easy to collect sample materials.
AU  - Wang, L.*
AU  - Zhang, Y.*
AU  - Liu, X.*
AU  - Zhao, X.*
AU  - Ouyang, Y.*
AU  - Qiu, G.*
AU  - Lv, W.*
AU  - Zheng, F.*
AU  - Wang, Q.*
AU  - Lu, X.*
AU  - Peng, X.*
AU  - Wu, T.*
AU  - Lehmann, R.
AU  - Wang, C.*
AU  - Jia, W.*
AU  - Xu, G.*
C1  - 60971
C2  - 49780
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 1005-1014
TI  - Metabolite triplet in serum improves the diagnostic accuracy of prediabetes and diabetes screening.
JO  - J. Proteome Res.
VL  - 20
IS  - 1
PB  - Amer Chemical Soc
PY  - 2021
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Bleomycin (BLM)-induced pulmonary fibrosis is characterized by inflammation in the alveoli, subsequent deposition of extracellular matrix (ECM) and myofibroblasts, and an impaired fibrinolytic system. Here, we describe major hematological changes, the IL-17A-mediated p53-fibrinolytic pathway, and the high throughput hits of liquid chromatography-mass spectrometry (LC-MS) analysis during the progression of pulmonary fibrosis and the therapeutic potential of curcumin against disease progression. C57BL/6 mice were exposed to BLM, followed by curcumin intervention after 24 and 48 h. Mice were sacrificed after 7 days to validate the hematological parameters, molecular pathways, and proteomics. Various techniques such as western blotting, immunofluorescence, reverse transcriptase polymerase chain reaction (RT-PCR), hematoxylin and eosin staining, Masson's trichrome staining, and immunohistochemistry were used to validate the proposed theory. LC-MS analysis was performed using a Q-Orbitrap mass spectrometer. The Schrodinger approach was used to perform the in silico molecular docking studies. BLM-exposed mice exhibited gradual weight loss and altered lung morphology; however, these were reversed by curcumin treatment. Significant changes in the hematological parameters confirmed the severity of BLM exposure in the mice, and expression of IL-17A-mediated p53-fibrinolytic system components and alveolar epithelial cell (AEC) apoptosis further confirmed the pathophysiology of pulmonary fibrosis. Differentially expressed proteins were characterized and mapped using the proteomics approach. A strong interaction of curcumin is observed with p53, uPA, and PAI-I proteins. The key role of IL-17A-mediated inflammation in the impairment of the p53-fibrinolytic system and AEC apoptosis was confirmed during BLM-induced pulmonary fibrosis. Therapeutic efficacy of curcumin exhibited a protective role against the progression of pulmonary fibrosis, which promises potent therapeutic modality to target the IL-17A-mediated p53-fibrinolytic system during pulmonary fibrosis.
AU  - Gouda, M.
AU  - Rex, D.A.B.*
AU  - Priya, S.E.S.*
AU  - Modi, P.K.*
AU  - Chanderasekaran, J.*
AU  - Bhandary, Y.P.*
C1  - 60032
C2  - 49179
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 2950-2963
TI  - Proteomics analysis revealed the importance of inflammation mediated downstream pathways and the protective role of curcumin during bleomycin-induced pulmonary fibrosis in C57BL/6 mice.
JO  - J. Proteome Res.
VL  - 19
IS  - 8
PB  - Amer Chemical Soc
PY  - 2020
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The impact of low-dose ionizing radiation (IR) on the human brain has recently attracted attention due to the increased use of IR for diagnostic purposes. The aim of this study was to investigate low-dose radiation response in the hippocampus. Female B6C3F1 mice were exposed to total body irradiation with 0 (control), 0.063, 0.125, or 0.5 Gy. Quantitative label-free proteomic analysis of the hippocampus was performed after 24 months. CREB signaling and CREB-associated pathways were affected at all doses. The lower doses (0.063 and 0.125 Gy) induced the CREB pathway, whereas the exposure to 0.5 Gy deactivated CREB. Similarly, the lowest dose (0.063 Gy) was anti-inflammatory, reducing the number of activated microglia. In contrast, induction of activated microglia and reactive astroglia was found at 0.5 Gy, suggesting increased inflammation and astrogliosis, respectively. The apoptotic markers BAX and cleaved CASP-3 and oxidative stress markers were increased only at the highest dose. Since the activated CREB pathway plays a central role in learning and memory, these data suggest neuroprotection at the lowest dose (0.063 Gy) but neurodegeneration at 0.5 Gy. The response to 0.5 Gy resembles alterations found in healthy aging and thus may represent radiation-induced accelerated aging of the brain.
AU  - Hladik, D.
AU  - Dalke, C.
AU  - von Toerne, C.
AU  - Hauck, S.M.
AU  - Azimzadeh, O.*
AU  - Philipp, J.
AU  - Ung, M.-C.
AU  - Schlattl, H.
AU  - Rößler, U.*
AU  - Graw, J.
AU  - Atkinson, M.J.
AU  - Tapio, S.
C1  - 57299
C2  - 47672
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 337-345
TI  - Creb signaling mediates dose-dependent radiation response in the murine hippocampus two years after total body exposure.
JO  - J. Proteome Res.
VL  - 19
IS  - 1
PB  - Amer Chemical Soc
PY  - 2020
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Identification of chronic kidney disease patients at risk of progressing to end-stage renal disease (ESRD) is essential for treatment decision-making and clinical trial design. Here, we explored whether proton nuclear magnetic resonance (NMR) spectroscopy of blood plasma improves the currently best performing kidney failure risk equation, the so-called Tangri score. Our study cohort comprised 4640 participants from the German Chronic Kidney Disease (GCKD) study, of whom 185 (3.99%) progressed over a mean observation time of 3.70 +/- 0.88 years to ESRD requiring either dialysis or transplantation. The original four-variable Tangri risk equation yielded a C statistic of 0.863 (95% CI, 0.831-0.900). Upon inclusion of NMR features by state-of-the-art machine learning methods, the C statistic improved to 0.875 (95% CI, 0.850-0.911), thereby outperforming the Tangri score in 94 out of 100 subsampling rounds. Of the 24 NMR features included in the model, creatinine, high-density lipoprotein, valine, acetyl groups of glycoproteins, and Ca2+-EDTA carried the highest weights. In conclusion, proton NMR-based plasma fingerprinting improved markedly the detection of patients at risk of developing ESRD, thus enabling enhanced patient treatment.
AU  - Zacharias, H.U.
AU  - Altenbuchinger, M.*
AU  - Schultheiss, U.T.*
AU  - Samol, C.*
AU  - Kotsis, F.*
AU  - Poguntke, I.*
AU  - Sekula, P.*
AU  - Krumsiek, J.
AU  - Köttgen, A.*
AU  - Spang, R.*
AU  - Oefner, P.J.*
AU  - Gronwald, W.*
C1  - 55748
C2  - 46570
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 1796–1805
TI  - A novel metabolic signature to predict the requirement of dialysis or renal transplantation in patients with chronic kidney disease.
JO  - J. Proteome Res.
VL  - 18
IS  - 4
PB  - Amer Chemical Soc
PY  - 2019
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Prolonged storage of biospecimen can lead to artificially altered metabolite concentrations and thus bias data analysis in metabolomics experiments. To elucidate the potential impact of long-term storage on the metabolite profile, a pooled human plasma sample was aliquoted and stored at 80 degrees C. During a time period of five years, 1012 of the aliquots were measured with the Biocrates AbsoluteIDQ p180 targeted-metabolomics assay at 193 time points. Modeling the concentration courses over time revealed that 55 out of 111 metabolites remained stable. The statistically significantly changed metabolites showed on average an increase or decrease of +13.7% or -14.5%, respectively. In detail, increased concentration levels were observed for amino acids (mean: +15.4%), the sum of hexoses (+7.9%), butyrylcarnitine (+9.4%), and some phospholipids mostly with chain lengths exceeding 40 carbon atoms (mean: +18.0%). Lipids tended to exhibit decreased concentration levels with the following mean concentration changes: acylcarnitines, -12.1%; lysophosphatidylcholines, -15.1%; diacyl-phosphatidylcholines, -17.0%; acyl-alkyl-phosphatidylcholines, -13.3%; sphingomye-lins, -14.8%. We conclude that storage of plasma samples at -80 degrees C for up to five years can lead to altered concentration levels of amino acids, acylcarnitines, glycerophospholipids, sphingomyelins, and the sum of hexoses. These alterations must be considered when analyzing metabolomics data from long-term epidemiological studies.
AU  - Haid, M.
AU  - Muschet, C.
AU  - Wahl, S.
AU  - Römisch-Margl, W.
AU  - Prehn, C.
AU  - Möller, G.
AU  - Adamski, J.
C1  - 52191
C2  - 43803
CY  - Washington
SP  - 203-211
TI  - Long-Term Stability of Human Plasma Metabolites during Storage at-80 degrees C.
JO  - J. Proteome Res.
VL  - 17
IS  - 1
PB  - Amer Chemical Soc
PY  - 2018
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Host cell proteins are inevitable contaminants of biopharmaceuticals. Here, we performed detailed analyses of the host cell proteome of moss (Physcomitrella patens) bioreactor supernatants using mass spectrometry and subsequent bioinformatics analysis. Distinguishing between the apparent secretome and intracellular contaminants, a complex extracellular proteolytic network including subtilisin-like proteases, metallo-proteases, and aspartic proteases was identified. Knockout of a subtilisin-like protease affected the overall extracellular proteolytic activity. Besides proteases, also secreted protease-inhibiting proteins such as serpins were identified. Further, we confirmed predicted cleavage sites of 40 endogenous signal peptides employing an N-terminomics approach. The present data provide novel aspects to optimize both product stability of recombinant biopharmaceuticals as well as their maturation along the secretory pathway. Data are available via ProteomeXchange with identifier PXDO09517.
AU  - Hoernstein, S.N.W.*
AU  - Fode, B.*
AU  - Wiedemann, G.*
AU  - Lang, D.
AU  - Niederkrüger, H.*
AU  - Berg, B.*
AU  - Schaaf, A.*
AU  - Frischmuth, T.*
AU  - Schlosser, A.*
AU  - Decker, E.L.*
AU  - Reski, R.*
C1  - 54570
C2  - 45671
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 3749-3760
TI  - Host cell proteome of Physcomitrella patens harbors proteases and protease inhibitors under bioproduction conditions.
JO  - J. Proteome Res.
VL  - 17
IS  - 11
PB  - Amer Chemical Soc
PY  - 2018
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - High-dose ionizing radiation is known to induce adverse effects such as inflammation and fibrosis in the heart. Transcriptional regulators PPARα and TGFβ are known to be involved in this radiation response. PPARα, an anti-inflammatory transcription factor controlling cardiac energy metabolism, is inactivated by irradiation. The pro-inflammatory and pro-fibrotic TGFβ is activated by irradiation via SMAD-dependent and SMAD-independent pathways. The goal of this study was to investigate how altering the level of PPARα influences the radiation response of these signaling pathways. For this purpose, we used genetically modified C57Bl/6 mice with wild type (+/+), heterozygous (+/-) or homozygous (-/-) PPARα genotype. Mice were locally irradiated to the heart using doses of 8 or 16 Gy; the controls were sham-irradiated. The heart tissue was investigated using label-free proteomics 20 weeks after the irradiation and the predicted pathways were validated using immunoblotting, ELISA, and immunohistochemistry. The heterozygous PPARα mice showed most radiation-induced changes in the cardiac proteome, whereas the homozygous PPARα mice showed the least changes. Irradiation induced SMAD-dependent TGFβ signaling independently of the PPARα status, but the presence of PPARα was necessary for the activation of the SMAD-independent pathway. These data indicate a central role of PPARα in cardiac response to ionizing radiation.
AU  - Subramanian, V.
AU  - Borchard, S.
AU  - Azimzadeh, O.
AU  - Sievert, W.
AU  - Merl-Pham, J.
AU  - Mancuso, M.*
AU  - Pasquali, E.*
AU  - Multhoff, G.
AU  - Popper, B.*
AU  - Zischka, H.
AU  - Atkinson, M.J.
AU  - Tapio, S.
C1  - 53900
C2  - 45139
SP  - 1677-1689
TI  - PPARα is necessary for radiation-induced activation of noncanonical TGFβ signaling in the heart.
JO  - J. Proteome Res.
VL  - 17
IS  - 4
PY  - 2018
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The pathophysiology underlying the autoimmune disease type 1 diabetes (T1D) is poorly understood. Obtaining an accurate proteomic profile of the T helper cell population is essential for understanding the pathogenesis of T1D. Here, we performed in-depth proteomic profiling of peripheral CD4+ T cells in a pediatric cohort to identify cellular signatures associated with the onset of T1D. Using only 250 000 CD4+ T cells per patient, isolated from biobanked PBMC samples, we identified nearly 6000 proteins using deep-proteome profiling with LC-MS/MS data independent acquisition. Our analysis revealed an inflammatory signature in patients with T1D; this signature is characterized by circulating mediators of neutrophils, platelets, and the complement system. This signature likely reflects the inflammatory extracellular milieu, which suggests that activation of the innate immune system plays an important role in disease onset. Our results emphasize the potential value of using high-resolution LC-MS/MS to investigate limited quantities of biobanked samples to identify disease-relevant proteomic patterns. Proteomic profiles of 114 individuals have been deposited in a comprehensive portable repository serving as a unique resource for CD4+ T cell expression in the context of both health and T1D disease.
AU  - Lepper, M.F.
AU  - Ohmayer, U.
AU  - von Toerne, C.
AU  - Maison, N.
AU  - Ziegler, A.-G.
AU  - Hauck, S.M.
C1  - 52454
C2  - 43984
CY  - Washington
SP  - 618-634
TI  - Proteomic landscape of patient-derived CD4+T cells in recent-onset type 1 diabetes.
JO  - J. Proteome Res.
VL  - 17
IS  - 1
PB  - Amer Chemical Soc
PY  - 2017
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step toward the comprehensive understanding of porcine biology, evolution, and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the functional and structural annotation of the Sus scrofa genome is far from complete. Here, we present mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 and 39 days after gestation. We found that the data provide evidence for and improve the annotation of 8176 protein-coding genes including 588 novel and 321 refined gene models. The analysis of tissue-specific proteins and the temporal expression profiles of embryonic proteins provides an initial functional characterization of expressed protein interaction networks and modules including as yet uncharacterized proteins. Comparative transcript and protein expression analysis to human organs reveal a moderate conservation of protein translation across species. We anticipate that this resource will facilitate basic and applied research on Sus scrofa as well as its porcine relatives.
AU  - Marx, H.*
AU  - Hahne, H.*
AU  - Ulbrich, S.E.*
AU  - Schnieke, A.*
AU  - Rottmann, O.*
AU  - Frishman, D.
AU  - Kuster, B.*
C1  - 51735
C2  - 43427
SP  - 2887-2898
TI  - Annotation of the domestic pig genome by quantitative proteogenomics.
JO  - J. Proteome Res.
VL  - 16
IS  - 8
PY  - 2017
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Radiation is the most common treatment of cancer. Minimizing the normal tissue injury, especially the damage to vascular endothelium, remains a challenge. This study aimed to analyze direct and indirect radiation effects on the endothelium by investigating mechanisms of signal transfer from irradiated to nonirradiated endothelial cells by means of secreted proteins. Human coronary artery endothelial cells (HCECest2) undergo radiation-induced senescence in vitro 14 days after exposure to 10 Gy X-rays. Proteomics analysis was performed on HCECest2 14 days after irradiation with X-ray doses of 0 Gy (control) or 10 Gy using label-free technology. Additionally, the proteomes of control and radiation-induced secretomes, and those of nonirradiated HCECest2 exposed for 24 h to secreted proteins of either condition were measured. Key changes identified by proteomics and bioinformatics were validated by immunoblotting, ELISA, bead-based multiplex assays, and targeted transcriptomics. The irradiated cells, their secretome, and the nonirradiated recipient cells showed similar inflammatory response, characterized by induction of interferon type I-related proteins and activation of the STAT3 pathway. These data indicate that irradiated endothelial cells may adversely affect nonirradiated surrounding cells via senescence-associated secretory phenotype. This study adds to our knowledge of the pathological background of radiation-induced cardiovascular disease.
AU  - Philipp, J.
AU  - Azimzadeh, O.
AU  - Subramanian, V.
AU  - Merl-Pham, J.
AU  - Lowe, D.*
AU  - Hladik, D.
AU  - Erbeldinger, N.*
AU  - Ktitareva, S.*
AU  - Fournier, C.*
AU  - Atkinson, M.J.
AU  - Raj, K.*
AU  - Tapio, S.
C1  - 52186
C2  - 43785
SP  - 3903-3916
TI  - Radiation-induced endothelial inflammation is transferred via the secretome to recipient cells in a STAT-mediated process.
JO  - J. Proteome Res.
VL  - 16
IS  - 10
PY  - 2017
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Blood is one of the most used biofluids in metabolomics studies, and the serum and plasma fractions are routinely used as a proxy for blood itself. Here we investigated the association networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ∼1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA–MS/MS. Four different inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain consensus networks. The plasma and serum networks obtained from different studies showed different topological properties with the serum network being more connected than the plasma network. On a global level, metabolite association networks from plasma and serum fractions obtained from the same blood sample of healthy people show similar topologies, and at a local level, some differences arise like in the case of amino acids.
AU  - Suarez-Diez, M.*
AU  - Adam, J.
AU  - Adamski, J.
AU  - Chasapi, S.A.*
AU  - Luchinat, C.*
AU  - Peters, A.
AU  - Prehn, C.
AU  - Santucci, C.*
AU  - Spyridonidis, A.*
AU  - Spyroulias, G.A.*
AU  - Tenori, L.*
AU  - Wang-Sattler, R.
AU  - Saccenti, E.*
C1  - 51155
C2  - 42776
CY  - Washington
SP  - 2547-2559
TI  - Plasma and serum metabolite association networks: Comparibility within and between studies using NMR and MS profiling.
JO  - J. Proteome Res.
VL  - 16
IS  - 7
PB  - Amer Chemical Soc
PY  - 2017
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Epidemiological data from patients undergoing radiotherapy for thoracic tumours clearly show the damaging effect of ionising radiation on cardiovascular system. The long-term impairment of heart function and structure after local high-dose irradiation is associated with systemic inflammatory response, contraction impairment, microvascular damage and cardiac fibrosis. The goal of the present study was to investigate molecular mechanisms involved in this process. C57BL/6J mice received a single X-ray dose of 16 Gy given locally to the heart at the age of 8 weeks. Radiation-induced changes in the heart transcriptome and proteome were investigated 40 weeks after the exposure. The omics data were analysed by bioinformatics tools and validated by immunoblotting. Integrated network analysis of transcriptomics and proteomics data elucidated the signalling pathways that were similarly affected at gene and protein level. Analysis showed induction of transforming growth factor (TGF) beta signalling but inactivation of peroxisome proliferator-activated receptor (PPAR) alpha signalling in irradiated heart. The putative mediator role of mitogen-activated protein kinase (MAPK) cascade linking PPAR alpha and TGF beta signalling was supported by data from immunoblotting and ELISA. This study indicates that both signalling pathways are involved in radiation-induced heart fibrosis, metabolic disordering and impaired contractility, a pathophysiological condition that is often observed in patients that received high radiation doses in thorax.
AU  - Subramanian, V.
AU  - Seemann, I.*
AU  - Merl-Pham, J.
AU  - Hauck, S.M.
AU  - Stewart, F.*
AU  - Atkinson, M.J.
AU  - Tapio, S.
AU  - Azimzadeh, O.
C1  - 49974
C2  - 41948
CY  - Washington
SP  - 307-318
TI  - The role of TGF beta and PPAR alpha signalling pathways in radiation response of locally exposed heart: Integrated global transcriptomics and proteomics analysis.
JO  - J. Proteome Res.
VL  - 16
IS  - 1
PB  - Amer Chemical Soc
PY  - 2017
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Preterm delivery (PTD) represents a major health problem that occurs in 1 in 10 births. The hypothesis of the present study was that the metabolic profile of different biological fluids, obtained from pregnant women during the second trimester of gestation, could allow useful correlations with pregnancy outcome. Holistic and targeted metabolomics approaches were applied for the complementary assessment of the metabolic content of prospectively collected amniotic fluid (AF) and paired maternal blood serum samples from 35 women who delivered preterm (between 29 weeks + 0 days and 36 weeks +5 days gestation) and 35 women delivered at term. The results revealed trends relating the metabolic content of the analyzed samples with preterm delivery. Untargeted and targeted profiling showed differentiations in certain key metabolites in the biological fluids of the two study groups. In AF, intermediate metabolites involved in energy metabolism (pyruvic acid, glutamic acid, and glutamine) were found to contribute to the classification of the two groups. In maternal serum, increased levels of lipids and alterations of key end-point metabolites were observed in cases of preterm delivery. Overall, the metabolic content of second-trimester AF and maternal blood serum shows potential for the identification of biomarkers related to fetal growth and preterm delivery.
AU  - Virgiliou, C.*
AU  - Gika, H.G.*
AU  - Witting, M.
AU  - Bletsou, A.A.*
AU  - Athanasiadis, A.*
AU  - Zafrakas, M.*
AU  - Thomaidis, N.S.*
AU  - Raikos, N.*
AU  - Makrydimas, G.*
AU  - Theodoridis, G.A.*
C1  - 50510
C2  - 42497
CY  - Washington
SP  - 898-910
TI  - Amniotic fluid and maternal serum metabolic signatures in the second trimester associated with preterm delivery.
JO  - J. Proteome Res.
VL  - 16
IS  - 2
PB  - Amer Chemical Soc
PY  - 2017
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The rd10 mouse is a model of retinitis pigmentosa characterized by the dysfunction of a rod-photoreceptor-specific phosphodiesterase. Compared to the rd1 mouse, retinal degeneration in the rd10 mouse begins later in age with a milder phenotype, making it ideal for investigating cell death and neuroprotective mechanisms. Alterations in the rd10 retina proteome at pre-, peak-, and post-degenerative time points were examined using a modified high-recovery filter-aided sample preparation (FASP) method in combination with label-free quantitative mass spectrometry, generating a proteomic dataset on almost 3000 proteins. Our data confirmed a period of protein expression similar to age-matched wild-type mice pre-degeneration, with decreases in proteins associated with phototransduction and increases in signaling proteins at peak- and post-degenerative stages. 57 proteins were differentially expressed in the rd10 retinae during peak-degeneration compared to wild-type mice after stringent FDR correction (q<0.05). Network analysis separated these proteins into a cluster of downregulated photoreceptor proteins, and one of upregulated signaling proteins centered around GFAP, STAT3, and STAT1. This is the first study to identify alterations in STAT1 in the rd10 mouse, which were confirmed with gene expression and immunoblotting experiments underpinning the efficacy of our approach. This unique proteomic dataset on protein dynamics during retinal degeneration could serve as an information source for vision research in the future.
AU  - Ly, A.
AU  - Merl-Pham, J.
AU  - Priller, M.
AU  - Gruhn, F.
AU  - Senninger, N.
AU  - Ueffing, M.
AU  - Hauck, S.M.
C1  - 48044
C2  - 39873
CY  - Washington
SP  - 1350-1359
TI  - Proteomic profiling suggests central role of STAT signaling during retinal degeneration in the rd10 mouse model.
JO  - J. Proteome Res.
VL  - 15
IS  - 4
PB  - Amer Chemical Soc
PY  - 2016
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - This study aims at identifying metabolites that significantly associate with self-reported joint symptoms (diagnostic) and metabolites that can predict the change from a symptom-free status to the development of self-reported joint symptoms after a 7 years period (prognostic). More than 300 metabolites were analyzed for 2246 subjects from the longitudinal study of the KORA (Cooperative Health Research in the Region of Augsburg, Germany), specifically the fourth survey S4 and its 7-year follow-up study F4. Two types of self-reported symptoms, chronic joint inflammation and worn out joints, were used for the analyses. Diagnostic analysis identified dysregulated metabolites in cases with symptoms compared with controls. Prognostic analysis identified metabolites that differentiate subjects in S4 who remained symptom-free after 7 years (F4) from those who developed any combination of symptoms. 48 metabolites were identified as nominally significantly (p < 0.05) associated with the self-reported symptoms in the diagnostic analysis, among which steroids show Bonferroni significance. 45 metabolites were identified as nominally significantly associated with developing symptoms after 7 years, among which hippurate showed Bonferroni significance. We show that metabolic profiles of self-reported joint symptoms are in line with metabolites known to associate with various forms of arthritis and suggest that future studies may benefit from that by investigating the possible use of self-reporting/questionnaire along with metabolic markers for the early referral of patients for further diagnostic workup and treatment of arthritis.
AU  - Yousri, N.A.*
AU  - Kastenmüller, G.
AU  - AlHaq, W.G.*
AU  - Holle, R.
AU  - Kääb, S.*
AU  - Mohney, R.P.*
AU  - Gieger, C.
AU  - Peters, A.
AU  - Adamski, J.
AU  - Suhre, K.
AU  - Arayssi, T.*
C1  - 47653
C2  - 39384
CY  - Washington
SP  - 554-562
TI  - Diagnostic and prognostic metabolites identified for joint symptoms in the KORA population.
JO  - J. Proteome Res.
VL  - 15
IS  - 2
PB  - Amer Chemical Soc
PY  - 2016
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Epidemiological data from radiotherapy patients show the damaging effect of ionizing radiation on heart and vasculature. The endothelium is the main target of radiation damage and contributes essentially to the development of cardiac injury. However, the molecular mechanisms behind the radiation-induced endothelial dysfunction are not fully understood. In the present study, 10-week-old C57Bl/6 mice received local X-ray heart doses of 8 or 16 Gy and were sacrificed after 16 weeks; the controls were sham-irradiated. The cardiac microvascular endothelial cells were isolated from the heart tissue using streptavidin-CD31-coated microbeads. The cells were lysed and proteins were labeled with duplex isotope-coded protein label methodology for quantification. All samples were analyzed by LC–ESI–MS/MS and Proteome Discoverer software. The proteomics data were further studied by bioinformatics tools and validated by targeted transcriptomics, immunoblotting, immunohistochemistry, and serum profiling. Radiation-induced endothelial dysfunction was characterized by impaired energy metabolism and perturbation of the insulin/IGF-PI3K-Akt signaling pathway. The data also strongly suggested premature endothelial senescence, increased oxidative stress, decreased NO availability, and enhanced inflammation as main causes of radiation-induced long-term vascular dysfunction. Detailed data on molecular mechanisms of radiation-induced vascular injury as compiled here are essential in developing radiotherapy strategies that minimize cardiovascular complications.
AU  - Azimzadeh, O.
AU  - Sievert, W.
AU  - Sarioglu, H.
AU  - Merl-Pham, J.
AU  - Yentrapalli, R.
AU  - Bakshi, M.V.
AU  - Janik, D.
AU  - Ueffing, M.
AU  - Atkinson, M.J.
AU  - Multhoff, G.
AU  - Tapio, S.
C1  - 43256
C2  - 36271
CY  - Washington
SP  - 1203-1219
TI  - Integrative proteomics and targeted transcriptomics analyses in cardiac endothelial cells unravel mechanisms of long-term radiation-induced vascular dysfunction.
JO  - J. Proteome Res.
VL  - 14
IS  - 2
PB  - Amer Chemical Soc
PY  - 2015
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Tens of thousands of people are being exposed daily to environmental low-dose gamma radiation. Epidemiological data indicate that such low radiation doses may negatively affect liver function and result in the development of liver disease. However, the biological mechanisms behind these adverse effects are unknown. The aim of this study was to investigate radiation-induced damage in the liver after low radiation doses. Neonatal male NMRI mice were exposed to total body irradiation on postnatal day 10 using acute single doses ranging from 0.02 to 1.0 Gy. Early (1 day) and late (7 months) changes in the liver proteome were tracked using isotope-coded protein label technology and quantitative mass spectrometry. Our data indicate that low and moderate radiation doses induce an immediate inhibition of the glycolysis pathway and pyruvate dehydrogenase availability in the liver. Furthermore, they lead to significant long-term alterations in lipid metabolism and increased liver inflammation accompanying inactivation of the transcription factor peroxisome proliferator-activated receptor alpha. This study contributes to the understanding of the potential risk of liver damage in populations environmentally exposed to ionizing radiation.
AU  - Bakshi, M.V.
AU  - Azimzadeh, O.
AU  - Barjaktarovic, Z.
AU  - Kempf, S.J.
AU  - Merl-Pham, J.
AU  - Hauck, S.M.
AU  - Buratovic, S.*
AU  - Eriksson, P.*
AU  - Atkinson, M.J.
AU  - Tapio, S.
C1  - 32538
C2  - 35114
CY  - Washington
SP  - 366-373
TI  - Total body exposure to low-dose ionizing radiation induces long-term alterations to the liver proteome of neonatally exposed mice.
JO  - J. Proteome Res.
VL  - 14
IS  - 1
PB  - Amer Chemical Soc
PY  - 2015
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Most studies investigating human metabolomics measurements are limited to a single biofluid, most often blood or urine. An organism's biochemical pool, however, comprises complex transboundary relationships, which can only be understood by investigating metabolic interactions and physiological processes spanning multiple parts of the human body. Therefore, we here propose a data-driven network-based approach to generate an integrated picture of metabolomics associations over multiple fluids. We performed an analysis of 2251 metabolites measured in plasma, urine, and saliva, from 374 participants of the Qatar Metabolomics Study on Diabetes (QMDiab). Gaussian graphical models (GGMs) were used to estimate metabolite-metabolite interactions on different subsets of the data set. First, we compared similarities and differences of the metabolome and the association networks between the three fluids. Second, we investigated the cross-talk between the fluids by analyzing correlations occurring between them. Third, we propose a framework for the analysis of medically relevant phenotypes by integrating type 2 diabetes, sex, age, and body mass index into our networks. In conclusion, we present a generic, data-driven network-based approach for structuring and visualizing metabolite correlations within and between multiple body fluids, enabling unbiased interpretation of metabolomics multifluid data.
AU  - Do, K.T.
AU  - Kastenmüller, G.
AU  - Mook-Kanamori, D.O.*
AU  - Yousri, N.A.*
AU  - Theis, F.J.
AU  - Suhre, K.
AU  - Krumsiek, J.
C1  - 42964
C2  - 35890
CY  - Washington
SP  - 1183-1194
TI  - Network-based approach for analyzing intra- and interfluid metabolite associations in human blood, urine, and saliva.
JO  - J. Proteome Res.
VL  - 14
IS  - 2
PB  - Amer Chemical Soc
PY  - 2015
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Despite the gut's longitudinal specialization for digestion and microbiome organization, most studies focus on the analysis of its end product, feces. To determine the metabolic and physiological functions of different sections of the gut, we aimed to define a comprehensive list of characteristic metabolites for the physiological gut sections and to quantify the selected pathways. We investigated the metabolic composition of seven different gut sections from four C57Bl/6N mice with nontargeted metabolite profiling using high-resolution NMR spectroscopy, which returned a comprehensive metabolite overview with a single analytical measurement per sample. Here we deliver a list of characteristic metabolites, describe metabolite changes along the gut, and highlight the site specificity for selected metabolite pathways. We find that the largest metabolic changes happen in the cecum, where the microbiome produces microbial metabolites. Furthermore, we show the evolution of bile acids along the gut and describe their site-specific conversion. We establish a metabolic basis for future investigations of metabolic perturbations, which can be introduced by dietary challenges or gene knockouts and provide valuable information for tailored study design and targeted sample collection.
AU  - Heinzmann, S.S.
AU  - Schmitt-Kopplin, P.
C1  - 44383
C2  - 36814
CY  - Washington
SP  - 2267-2277
TI  - Deep metabotyping of the murine gastrointestinal tract for the visualization of digestion and microbial metabolism.
JO  - J. Proteome Res.
VL  - 14
IS  - 5
PB  - Amer Chemical Soc
PY  - 2015
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The increased use of radiation-based medical imaging methods such as computer tomography is a matter of concern due to potential radiation-induced adverse effects. Efficient protection against such detrimental effects has not been possible due to inadequate understanding of radiation-induced alterations in signaling pathways. The aim of this study was to elucidate the molecular mechanisms behind learning and memory deficits after acute low and moderate doses of ionizing radiation. Female C57BL/6J mice were irradiated on postnatal day 10 (PND10) with gamma doses of 0.1 or 0.5 Gy. This was followed by evaluation of the cellular proteome, pathway-focused transcriptome, and neurological development/disease-focused miRNAome of hippocampus and cortex 24 h postirradiation. Our analysis showed that signaling pathways related to mitochondrial and synaptic functions were changed by acute irradiation. This may lead to reduced mitochondrial function paralleled by enhanced number of dendritic spines and neurite outgrowth due to elevated long-term potentiation, triggered by increased phosphorylated CREB. This was predominately observed in the cortex at 0.1 and 0.5 Gy and in the hippocampus only at 0.5 Gy. Moreover, a radiation-induced increase in the expression of several neural miRNAs associated with synaptic plasticity was found. The early changes in signaling pathways related to memory formation may be associated with the acute neurocognitive side effects in patients after brain radiotherapy but might also contribute to late radiation-induced cognitive injury.
AU  - Kempf, S.J.
AU  - Mörtl, S.
AU  - Sepe, S.*
AU  - von Toerne, C.
AU  - Hauck, S.M.
AU  - Atkinson, M.J.
AU  - Mastroberardino, P.G.*
AU  - Tapio, S.
C1  - 44381
C2  - 36811
CY  - Washington
SP  - 2055-2064
TI  - Low-dose ionizing radiation rapidly affects mitochondrial and synaptic signaling pathways in murine hippocampus and cortex.
JO  - J. Proteome Res.
VL  - 14
IS  - 5
PB  - Amer Chemical Soc
PY  - 2015
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Recent epidemiological data indicate that radiation doses as low as those used in computer tomography may result in long-term neurocognitive side effects. The aim of this study was to elucidate long-term molecular alterations related to memory formation in the brain after low and moderate doses of gamma radiation. Female C57BL/6J mice were irradiated on postnatal day 10 with total body doses of 0.1 Gy, 0.5 Gy or 2.0 Gy; the control group was sham-irradiated. The proteome analysis of hippocampus, cortex and synaptosomes isolated from these brain regions indicated changes in ephrin-related, RhoGDI and axonal guidance signalling.. Immunoblotting and miRNA-quantification demonstrated an imbalance in the synapse morphology-related Rac1-Cofilin pathway and long-term potentiation-related CREB signalling. Proteome profiling also showed impaired oxidative phosphorylation, especially in the synaptic mitochondria. This was accompanied by an early (4 weeks) reduction of mitochondrial respiration capacity in the hippocampus. Although the respiratory capacity was restored by 24 weeks, the number of deregulated mitochondrial complex proteins was increased at this time. All observed changes were significant at doses of 0.5 Gy and 2.0 Gy but not at 0.1 Gy. This study strongly suggests that ionising radiation at the neonatal state triggers persistent proteomic alterations associated with synaptic impairment.
AU  - Kempf, S.J.
AU  - Sepe, S.*
AU  - von Toerne, C.
AU  - Janik, D.
AU  - Neff, F.
AU  - Hauck, S.M.
AU  - Atkinson, M.J.
AU  - Mastroberardino, P.G.*
AU  - Tapio, S.
C1  - 46961
C2  - 39090
SP  - 4674-4686
TI  - Neonatal irradiation leads to persistent proteome alterations involved in synaptic plasticity in the mouse hippocampus and cortex.
JO  - J. Proteome Res.
VL  - 14
IS  - 11
PY  - 2015
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - MALDI mass spectrometry imaging (MSI) has rapidly established itself as a powerful biomarker discovery tool. To date, no formal investigation has assessed the center-to-center comparability of MALDI MSI experiments, an essential step for it to develop into a new diagnostic method. To test such capabilities, we have performed a multicenter study focused on biomarkers of stromal activation in breast cancer. MALDI MSI experiments were performed in two centers using independent tissue banks, infrastructure, methods, and practitioners. One of the data sets was used for discovery and the other for validation. Areas of intra- and extratumoral stroma were selected, and their protein signals were compared. Four protein signals were found to be significantly associated with tumor-associated stroma in the discovery data set measured in Munich. Three of these peaks were also detected in the independent validation data set measured in Leiden, all of which were also significantly associated with intratumoral stroma. Hierarchical clustering displayed 100% accuracy in the Munich MSI data set and 80.9% accuracy in the Leiden MSI data set. The association of one of the identified mass signals (PA28) with stromal activation was confirmed with immunohistochemistry performed on 20 breast tumors. Independent and international MALDI MSI investigations could identify validated biomarkers of stromal activation.
AU  - Dekker, T.J.*
AU  - Balluff, B.D.*
AU  - Jones, E.A.*
AU  - Schöne, C.D.*
AU  - Schmitt, M.*
AU  - Aubele, M.
AU  - Kroep, J.R.*
AU  - Smit, V.T.*
AU  - Tollenaar, R.A.*
AU  - Mesker, W.E.*
AU  - Walch, A.K.
AU  - McDonnell, L.A.*
C1  - 31233
C2  - 34224
SP  - 4730-4738
TI  - Multicenter Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI) identifies proteomic differences in breast-cancer-associated stroma.
JO  - J. Proteome Res.
VL  - 13
IS  - 11
PY  - 2014
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The clinical application of mass spectrometry imaging has developed into a sizeable sub-discipline of proteomics and metabolomics because its seamless integration with pathology enables biomarkers and biomarker profiles to be determined that can aid patient and disease stratification (diagnosis, prognosis and response to therapy). Confident identification of the discriminating peaks remains a challenge owing to the presence of non-tryptic protein fragments, large mass-to-charge ratio ions that are not efficiently fragmented via tandem mass spectrometry or a high density of isobaric species. To aid the clinical development and implementation of mass spectrometry imaging a public database of identifications has been initiated. The MSiMass list database (www.maldi-msi.org/mass) enables users to assign identities to the peaks observed in their experiments and provides the methods by which the identifications were obtained. In contrast to existing protein databases, this list is designed as a community effort without a formal review panel. In this concept, authors can freely enter data, and can comment on existing entries. In such, the database itself is an experiment on sharing knowledge and its ability to rapidly provide quality data will be evaluated in the future.
AU  - McDonnell, L.A.*
AU  - Walch, A.K.
AU  - Stoeckli, M.*
AU  - Corthals, G.L.*
C1  - 28631
C2  - 33503
CY  - Washington
SP  - 1138–1142
TI  - MSiMass list: A public database of identifications for protein MALDI MSI.
JO  - J. Proteome Res.
VL  - 13
IS  - 2
PB  - Amer. Chemical Soc.
PY  - 2014
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Genetic and environmental factors mediate via different physiological and molecular processes a shifted energy balance leading to overweight and obesity. To get insights in the underlying processes involved in energy intake and weight gain, we compared hypothalamic tissue of mice kept on a high-fat or control diet for 10 days by a proteomic approach. Using 2D difference gel electrophoresis in combination with LC-MS/MS, we observed significant abundance changes in 15 protein spots. One isoform of the protein DJ-1 was elevated in the high-fat diet group in the analyzed three different mouse strains SWR/J, C57BL/6N and AKR/J. Large scale validation of DJ-1 isoforms in individual samples and tissues confirmed a shift in the pattern of DJ-1 isoforms towards more acidic isoforms in several brain and peripheral tissues after feeding a high-fat diet for 10 days. The identification of an oxidation of cysteine 106 as well as a 2-succinyl modification of the same residue by mass spectrometry not only explains the isoelectric shift of DJ-1 but also links our results to similar shifts of DJ- 1 observed in neurodegenerative disease states under oxidative stress. We hypothesize that DJ-1 is a common physiological sensor involved in both nutrition-induced effects and neurodegenerative disease states.
AU  - Poschmann, G.*
AU  - Seyfarth, K.*
AU  - Besong Agbo, D.*
AU  - Klafki, H.-W.*
AU  - Rozman, J.
AU  - Wurst, W.
AU  - Wiltfang, J.*
AU  - Meyer, H.E.*
AU  - Klingenspor, M.
AU  - Stühler, K.*
C1  - 30830
C2  - 33905
CY  - Washington
SP  - 2339-2351
TI  - High fat diet induced isoform changes of the Parkinson’s disease protein DJ-1.
JO  - J. Proteome Res.
VL  - 13
IS  - 5
PB  - Amer Chemical Soc
PY  - 2014
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Biogenic isoprene (2-methyl-1,3-butadiene) improves the integrity and functionality of thylakoid membranes and scavenges reactive oxygen species (ROS) in plant tissue under stress conditions. On the basis of available physiological studies, we hypothesized that the suppression of isoprene production in the poplar plant by genetic engineering would cause changes in the chloroplast protein pattern, which in turn would compensate for changes in chloroplast functionality and overall plant performance under abiotic stress. To test this hypothesis, we used a stable isotope-coded protein-labeling technique in conjunction with polyacrylamide gel electrophoresis and liquid chromatography tandem mass spectrometry. We analyzed quantitative and qualitative changes in the chloroplast proteome of isoprene-emitting and non isoprene-emitting poplars. Here we demonstrate that suppression of isoprene synthase by RNA interference resulted in decreased levels of chloroplast proteins involved in photosynthesis and increased levels of histones, ribosomal proteins, and proteins related to metabolism. Overall, our results show that the absence of isoprene triggers a rearrangement of the chloroplast protein profile to minimize the negative stress effects resulting from the absence of isoprene. The present data strongly support the idea that isoprene improves/stabilizes thylakoid membrane structure and interferes with the production of ROS.
AU  - Velikova, V.B.
AU  - Ghirardo, A.
AU  - Vanzo, E.
AU  - Merl, J.
AU  - Hauck, S.M.
AU  - Schnitzler, J.-P.
C1  - 31182
C2  - 34302
CY  - Washington
SP  - 2005-2018
TI  - Genetic manipulation of isoprene emissions in poplar plants remodels the chloroplast proteome.
JO  - J. Proteome Res.
VL  - 13
IS  - 4
PB  - Amer Chemical Soc
PY  - 2014
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - A metabolic disorder such as Type 2 Diabetes mellitus (T2DM) is a complex disease induced by genetic, environmental and nutritional factors. The db/db mouse model, bearing a non-functional leptin receptor is widely used to investigate the pathophysiology of T2DM. Fecal extracts of db/db and wild type littermates were studied to unravel a broad spectrum of new and relevant metabolites related to T2DM as proxies of the interplay of gut microbiome and murine metabolomes. The non-targeted metabolomics approach consists of an integrated analytical concept of high-resolution mass spectrometry FT-ICR-MS followed by UPLC-TOF-MS/MS experiments. We demonstrate that a metabolic disorder such as T2DM affects the gastrointestinal tract environment thereby influencing different metabolic pathways and their respective metabolites in diabetic mice. Fatty acids, bile acids concerning cholic and deoxycholic acid and steroid metabolism were highly discriminative comparing fecal metabolomes of wt and db/db mice. Furthermore, sulfur-(S)-containing metabolites including N-acyl taurines were altered in diabetic mice, enabling to focus on S-containing metabolites, especially the sulfate and taurine conjugates of bile and fatty acids. Different sulfate containing bile acids including sulfocholic acid, oxocholic acid sulfate, taurocholic acid sulfate and cyprinol sulfate were significantly altered in diabetic mice. Moreover, we identified twelve new sulfate and taurine conjugates of hydroxylated fatty acids with significant importance in T2DM metabolism in db/db mice.
AU  - Walker, A.
AU  - Lucio, M.
AU  - Pfitzner, B.
AU  - Scheerer, M.F.
AU  - Neschen, S.
AU  - Hrabě de Angelis, M.
AU  - Hartmann, A.
AU  - Schmitt-Kopplin, P.
C1  - 31736
C2  - 34698
CY  - Washington
SP  - 4220-4231
TI  - The importance of sulfur-containing metabolites in discriminating fecal extracts between normal and type 2 diabetic mice.
JO  - J. Proteome Res.
VL  - 13
IS  - 10
PB  - Amer Chemical Soc
PY  - 2014
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Radiation exposure of the thorax is associated with a markedly increased risk of cardiac morbidity and mortality with a latency period of decades. Although many studies have confirmed the damaging effect of ionizing radiation on the myocardium and cardiac endothelial structure and function, the molecular mechanism behind this damage is not yet elucidated. Peroxisome proliferator-activated receptor alpha (PPAR alpha), a transcriptional regulator of lipid metabolism in heart tissue, has recently received great attention in the development of cardiovascular disease. The goal of this study was to investigate radiation-induced cardiac damage in general and the role of PPAR alpha in this process in particular. C57BL/6 mice received local heart irradiation with X-ray doses of 8 and 16 gray (Gy) at the age of 8 weeks. The mice were sacrificed 16 weeks later. Radiation-induced changes in the cardiac proteome were quantified using the Isotope Coded Protein Label (ICPL) method followed by mass spectrometry and software analysis. Significant alterations were observed in proteins involved in lipid metabolism and oxidative phosphorylation. Ionizing radiation markedly changed the phosphorylation and ubiquitination status of PPAR alpha. This was reflected as decreased expression of its target genes involved in energy metabolism and mitochondrial respiratory chain confirming the proteomics data. This study suggests that persistent alteration of cardiac metabolism due to impaired PPAR alpha activity contributes to the heart pathology after radiation.
AU  - Azimzadeh, O.
AU  - Sievert, W.*
AU  - Sarioglu, H.
AU  - Yentrapalli, R.
AU  - Barjaktarovic, Z.
AU  - Sriharshan, A.
AU  - Ueffing, M.
AU  - Janik, D.
AU  - Aichler, M.
AU  - Atkinson, M.J.
AU  - Multhoff, G.*
AU  - Tapio, S.
C1  - 24262
C2  - 31349
SP  - 2700-2714
TI  - PPAR alpha: A novel radiation target in locally exposed Mus musculus heart revealed by quantitative proteomics.
JO  - J. Proteome Res.
VL  - 12
IS  - 6
PB  - Amer. Chemical Soc.
PY  - 2013
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Autoimmune uveitis is characterized by crossing of blood-retinal barrier (BRB) by autoaggressive immune cells. Equine recurrent uveitis (ERU) is a valuable spontaneous model for autoimmune uveitis and analyses of differentially expressed proteins in ERU unraveled changed protein clusters in target tissues and immune system. Healthy eyes are devoid of leukocytes. In ERU, however, leukocytes enter the inner eye and subsequently destroy it. Molecular mechanisms enabling cell migration through BRB still remain elusive. Previously, we detected decreased talin 1 expression in blood-derived granulocytes of ERU cases, linking the innate immune system to ERU. Because changes in leukocyte protein expression pattern may play a role in pathological abnormalities leading to migration ability, we aimed at identifying interactors of talin 1 in leukocytes with immunoprecipitation, followed by LC-MS/MS for candidate identification. This enabled us to identify CD90 (Thy1) as novel interactor of talin 1 besides several other interactors. In blood-derived granulocytes from healthy individuals, CD90 was highly abundant and significantly reduced in ERU, especially in effector cells. Connection between talin 1 and CD90 and their expression differences in inflammation is an interesting novel finding allowing deeper insight into immune response of innate immune system and granulocyte migration ability in this organ-specific autoimmune disease.
AU  - Degroote, R.L.*
AU  - Hauck, S.M.
AU  - Treutlein, G.*
AU  - Amann, B.*
AU  - Fröhlich, K.J.H.*
AU  - Kremmer, E.
AU  - Merl, J.
AU  - Stangassinger, M.*
AU  - Ueffing, M.
AU  - Deeg, C. A.*
C1  - 28243
C2  - 33027
SP  - 5812–5819
TI  - Expression changes and novel interaction partners of talin 1 in effector cells of autoimmune uveitis.
JO  - J. Proteome Res.
VL  - 12
IS  - 12
PB  - Amer. Chemnical Soc.
PY  - 2013
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Most autoimmune diseases are multifactorial diseases and are caused by the immunological reaction against a number of autoantigens. Key for understanding autoimmune pathologies is the knowledge of the targeted autoantigens, both initially and during disease progression. We present an approach for autoantigen identification based on isolation of intact autoantibody-antigen complexes from body fluids. After organic precipitation of high molecular weight proteins and free immunoglobulins, released autoantigens were identified by quantitative label-free liquid chromatography mass spectrometry. We confirmed feasibility of target enrichment and identification from highly complex body fluid proteomes by spiking of a pre-defined antigen-antibody complex at low level of abundance. As a proof of principle we studied the blinding disease autoimmune uveitis, which is caused by autoreactive T-cells attacking the inner eye and is accompanied by autoantibodies. We identified three novel autoantigens in the spontaneous animal model equine recurrent uveitis (secreted acidic phosphoprotein osteopontin, extracellular matrix protein 1 and metalloproteinase inhibitor 2) and confirmed presence of the corresponding autoantibodies in 15 - 25% of patient samples by enzyme-linked immunosorbent assay. Thus, this workflow led to the identification of novel autoantigens in autoimmune uveitis and may provide a versatile and useful tool to identify autoantigens in other autoimmune diseases in future.
AU  - Merl, J.
AU  - Deeg, C.A.*
AU  - Swadzba, M.E.*
AU  - Ueffing, M.
AU  - Hauck, S.M.
C1  - 27584
C2  - 32733
CY  - Washington
SP  - 5656-5665
TI  - Identification of autoantigens in body fluids by combining pull-downs and organic precipitations of intact immune complexes with quantitative label-free mass spectrometry.
JO  - J. Proteome Res.
VL  - 12
IS  - 12
PB  - Amer Chemical Soc
PY  - 2013
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - A comprehensive quantitative analysis of changes in protein phosphorylation preceding or accompanying transcriptional activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in 5L rat hepatoma cells was performed using the SILAC approach. Following exposure of the cells to DMSO or 1 nM TCDD for 0.5 to 2 h, 5648 phosphorylated peptides corresponding to 2156 phosphoproteins were identified. Eight peptides exhibited a statistically significantly altered phosphorylation because of TCDD exposure and 22 showed a regulation factor of ≥1.5 in one of the experiments per time point. The vast majority of the TCCD-induced phosphorylation changes had not been reported before. The transcription factor ARNT, the obligate partner for gene activation by the TCDD-bound Ah receptor, exhibited an up-regulation of its Ser77 phosphorylation, a modification known to control the differential binding of ARNT homodimers and heterodimers to different enhancers suggesting that this phosphorylation represents a novel mechanism contributing to the alteration of gene expression by TCDD. Other proteins with altered phosphorylation included, among others, various transcriptional coregulators previously unknown to participate in TCDD-induced gene activation, regulators of small GTPases of the Ras superfamily, UBX domain-containing proteins and the oncogenic protein LYRIC. The results open up new directions for research on the molecular mechanisms of dioxin action and toxicity.
AU  - Schulz, M.
AU  - Brandner, S.
AU  - Eberhagen, C.
AU  - Eckardt-Schupp, F.
AU  - Larsen, M.R.*
AU  - Andrae, U.
C1  - 22778
C2  - 30936
SP  - 866-882
TI  - Quantitative phosphoproteomic analysis of early alterations in protein phosphorylation by 2,3,7,8-tetrachlorodibenzo-p-dioxin.
JO  - J. Proteome Res.
VL  - 12
IS  - 2
PB  - American Chemical Society
PY  - 2013
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Male New Zealand Obese (NZO) mice progress through pathophysiological stages similar to humans developing obesity-associated type 2 diabetes (T2D). The current challenge is to establish quantitative proteomics from small plasma sample amounts. We established an analytical workflow that facilitates a reproducible depletion of high-abundance proteins, has high throughput applicability, and allows absolute quantification of proteins from mouse plasma samples by LC-SRM-MS. The ProteoMiner equalizing technology was adjusted to the small sample amount and reproducibility of the identifications was monitored by spike proteins. Based on the label-free relative quantification of proteins in depleted plasma of a test set of NZO mice, assays for potential candidates were designed for the setup of a targeted selected reaction monitoring (SRM) approach and absolute quantification. We could demonstrate that apolipoprotein E (Apoe), mannose-binding lectin 2 (Mbl2) and parotid secretory protein (Psp) are present at significantly different quantities in depleted plasma of diabetic NZO mice compared to non-diabetic controls using AQUA peptides. Quantification was validated for Mbl2 using the ELISA technology on non-depleted plasma. We conclude that the depletion technique is applicable to restricted sample amounts and suitable for the identification of T2D signatures in plasma.
AU  - von Toerne, C.
AU  - Kahle-Stephan, M.
AU  - Schäfer, A.
AU  - Ispiryan, R.
AU  - Blindert, M.
AU  - Hrabě de Angelis, M.
AU  - Neschen, S.
AU  - Ueffing, M.
AU  - Hauck, S.M.
C1  - 11901
C2  - 30845
SP  - 1331-1343
TI  - Apoe, Mbl2 and Psp plasma protein levels correlate with diabetic phenotype in NZO mice - an optimized rapid workflow for SRM-based quantification.
JO  - J. Proteome Res.
VL  - 12
IS  - 3
PB  - American Chemical Society
PY  - 2013
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Protein degradation by the ubiquitin proteasome system ensures controlled degradation of structural proteins, signaling mediators, and transcription factors. Inhibition of proteasome function by specific proteasome inhibitors results in dose-dependent cellular effects ranging from induction of apoptosis to protective stress responses. The present study seeks to identify nuclear regulators mediating the protective stress response to low dose proteasome inhibition. Primary human endothelial cells were treated with low doses of the proteasome inhibitor MG132 for 2 h, and proteomic analysis of nuclear extracts was performed. Using a 2-D differential in gel electrophoresis (DIGE) approach, we identified more than 24 splice factors to be differentially regulated by low dose proteasome inhibition. In particular, several isoforms of hnRNPA1 were shown to be increased, pointing toward altered posttranslational modification of hnRNPA1 upon proteasome inhibition. Elevated levels of splice factors were associated with a different alternative splicing pattern in response to proteasome inhibition as determined by Affymetrix exon array profiling. Of note, we observed alternative RNA processing for stress associated genes such as caspases and heat shock proteins. Our study provides first evidence that low dose proteasome inhibition affects posttranscriptional regulation of splice factors and early alternative splicing events.
AU  - Bieler, S.*
AU  - Hammer, E.*
AU  - Gesell-Salazar, M.*
AU  - Völker, U.*
AU  - Stangl, K.*
AU  - Meiners, S.
C1  - 8206
C2  - 30048
SP  - 3947-3954
TI  - Low dose proteasome inhibition affects alternative splicing.
JO  - J. Proteome Res.
VL  - 11
IS  - 8
PB  - American Chemical Society
PY  - 2012
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The quality of human tissue specimens can have a significant impact on analytical data sets for biomarker research. The aim of this study was to characterize fluctuations of protein and phosphoprotein levels in human tissue samples during the preanalytical phase. Eleven intestine and 17 liver specimens were surgically resected, aliquoted, and either snap-frozen or fixed in formalin immediately or exposed to different ischemic conditions before preservation. Protein levels in the resultant samples were investigated by reverse phase protein array, Western blot analysis, and liquid chromatography-tandem mass spectrometry. Our data revealed that the degree of sensitivity of proteins and phosphoproteins to delayed preservation varied between different patients and tissue types. For example, up-regulation of phospho-p42/44 MAPK in intestine samples was seen in some patients but not in others. General trends toward up- or down-regulation of most proteins were not evident due to pronounced interpatient variability but signal intensities of only a few proteins, such as cytokeratin 18, were altered from baseline in postresection samples. In contrast, glyceraldehyde 3-phosphate dehydrogenase was found to be stable during periods of cold ischemia. Our study represents a proper approach for studying potential protein fluctuations in tissue specimens for future biomarker development programs.
AU  - Gündisch, S.*
AU  - Hauck, S.M.
AU  - Sarioglu, H.
AU  - Schott, C.*
AU  - Viertler, C.*
AU  - Kap, M.*
AU  - Schuster, T.*
AU  - Reischauer, B.*
AU  - Rosenberg, R.*
AU  - Verhoef, C.*
AU  - Mischinger, H.-J.*
AU  - Riegman, P.*
AU  - Zatloukal, K.*
AU  - Becker, K.-F.*
C1  - 11047
C2  - 30478
SP  - 5748-5762
TI  - Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase.
JO  - J. Proteome Res.
VL  - 11
IS  - 12
PB  - American Chemical Assoc.
PY  - 2012
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Interpreting the complex interplay of metabolites in heterogeneous biosamples still poses a challenging task. In this study, we propose independent component analysis (ICA) as a multivariate analysis tool for the interpretation of large-scale metabolomics data. In particular, we employ a Bayesian ICA method based on a mean-field approach, which allows us to statistically infer the number of independent components to be reconstructed. The advantage of ICA over correlation-based methods like principal component analysis (PCA) is the utilization of higher order statistical dependencies, which not only yield additional information but also allow a more meaningful representation of the data with fewer components. We performed the described ICA approach on a large-scale metabolomics data set of human serum samples, comprising a total of 1764 study probands with 218 measured metabolites. Inspecting the source matrix of statistically independent metabolite profiles using a weighted enrichment algorithm, we observe strong enrichment of specific metabolic pathways in all components. This includes signatures from amino acid metabolism, energy-related processes, carbohydrate metabolism, and lipid metabolism. Our results imply that the human blood metabolome is composed of a distinct set of overlaying, statistically independent signals. ICA furthermore produces a mixing matrix, describing the strength of each independent component for each of the study probands. Correlating these values with plasma high-density lipoprotein (HDL) levels, we establish a novel association between HDL plasma levels and the branched-chain amino acid pathway. We conclude that the Bayesian ICA methodology has the power and flexibility to replace many of the nowadays common PCA and clustering-based analyses common in the research field.
AU  - Krumsiek, J.
AU  - Suhre, K.
AU  - Illig, T.
AU  - Adamski, J.
AU  - Theis, F.J.
C1  - 8327
C2  - 30059
SP  - 4120-4131
TI  - Bayesian independent component analysis recovers pathway signatures from blood metabolomics data.
JO  - J. Proteome Res.
VL  - 11
IS  - 8
PB  - Amer. Chemical Soc.
PY  - 2012
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - In clinical diagnostics, it is of outmost importance to correctly identify the source of a metastatic tumor, especially if no apparent primary tumor is present. Tissue-based proteomics might allow correct tumor classification. As a result, we performed MALDI imaging to generate proteomic signatures for different tumors. These signatures were used to classify common cancer types. At first, a cohort comprised of tissue samples from six adenocarcinoma entities located at different organ sites (esophagus, breast, colon, liver, stomach, thyroid gland, n = 171) was classified using two algorithms for a training and test set. For the test set, Support Vector Machine and Random Forest yielded overall accuracies of 82.74 and 81.18%, respectively. Then, colon cancer liver metastasis samples (n = 19) were introduced into the classification. The liver metastasis samples could be discriminated with high accuracy from primary tumors of colon cancer and hepatocellular carcinoma. Additionally, colon cancer liver metastasis samples could be successfully classified by using colon cancer primary tumor samples for the training of the classifier. These findings demonstrate that MALDI imaging-derived proteomic classifiers can discriminate between different tumor types at different organ sites and in the same site.
AU  - Meding, S.
AU  - Nitsche, U.*
AU  - Balluff, B.
AU  - Elsner, M.
AU  - Rauser, S.
AU  - Schöne, C.
AU  - Nipp, M.
AU  - Maak, M.*
AU  - Feith, M.*
AU  - Ebert, M.P.*
AU  - Friess, H.*
AU  - Langer, R.*
AU  - Höfler, H.
AU  - Zitzelsberger, H.
AU  - Rosenberg, R.*
AU  - Walch, A.K.
C1  - 7307
C2  - 29668
SP  - 1996-2003
TI  - Tumor classification of six common cancer types based on proteomic profiling by MALDI imaging.
JO  - J. Proteome Res.
VL  - 11
IS  - 3
PB  - Amer. Chemical Soc.
PY  - 2012
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The aim of this study was to use a two steps strategy metabolomics to screen/identify and validate novel metabolic biomarker(s) for epithelial ovarian cancer (EOC). In the screening step, serum samples from 27 healthy women, 28 benign ovarian tumors, and 29 EOCs were analyzed by using LC-MS based nontargeted metabolomics. The three groups were separated with OSC filtered PLS-DA model, and six metabolites (27-nor-5β-cholestane-3,7,12,24,25 pentol glucuronide (CPG), phenylalanine, glycocholic acid, propionylcarnitine, Phe-Phe and Lyso PC (18:2)) were considered as potential biomarker candidates. In the validation step, the six metabolites were analyzed in targeted metabolomics by LC-selective ion monitoring mass spectrometry in another 685 serum samples with various clinical backgrounds. As a result, CPG was evaluated to be a potential biomarker and its content was elevated in EOC tissues compared with benign ovarian tumor tissues (p = 0.0005). Besides, CPG levels were found to be up-regulated in early stage EOC and in the three types of EOC histological types. Other variables such as nonovarian diseases, medicine consumption, gynecological inflammations, and menopausal state did not interfere in using CPG as diagnosis marker. CPG was found to be complementary to CA125. Our findings suggest that CPG can be considered a statistical relevant biomarker of EOC, ready for early stage detection.
AU  - Chen, J.*
AU  - Zhang, X.Y.*
AU  - Cao, R.*
AU  - Lu, X.*
AU  - Zhao, S.M.*
AU  - Fekete, A.
AU  - Huang, Q.*
AU  - Schmitt-Kopplin, P.
AU  - Wang, Y.S.*
AU  - Xu, Z.L.*
AU  - Wan, X.P.*
AU  - Wu, X.H.*
AU  - Zhao, N.Q.*
AU  - Xu, C.J.*
AU  - Xu, G.W.*
C1  - 6294
C2  - 28331
SP  - 2625-2632
TI  - Serum 27-nor-5β-Cholestane-3,7,12,24,25 pentol glucuronide discovered by metabolomics as potential diagnostic biomarker for epithelium ovarian cancer.
JO  - J. Proteome Res.
VL  - 10
IS  - 5
PB  - Amer Chemical Soc
PY  - 2011
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Formalin-fixed paraffin-embedded (FFPE) tissue has recently gained interest as an alternative to fresh/frozen tissue for retrospective protein biomarker discovery. However, during the fixation process, proteins undergo degradation and cross-linking, making conventional protein analysis technologies problematic. In this study, we have compared several extraction and separation methods for the analysis of proteins in FFPE tissues. Incubation of tissue sections at high temperature with a novel extraction buffer (20 mM Tris-HCl, pH 8.8, 2% SDS, 1% beta-octylglucoside, 200 mM DTT, 200 mM glycine, and a mixture of protease inhibitors) resulted in improved protein recovery. Protein separation by 1-DE followed by LC-ESI MS/MS analysis was the most effective approach to identify proteins, based on the number of peptides reliably identified. Interestingly, a number of peptides were identified in regions of the 1DE not corresponding to their native molecular weights. This is an indication of the formation of protein-protein complexes by cross-linking, and of protein fragmentation due to prolonged sample storage. This study will facilitate the development of future proteomic analysis of FFPE tissue and provide a tool for the validation in archival samples of biomarkers of exposure, prognosis and disease.
AU  - Azimzadeh, O.
AU  - Barjaktarovic, Z.
AU  - Aubele, M.
AU  - Calzada-Wack, J.
AU  - Sarioglu, H.
AU  - Atkinson, M.J.*
AU  - Tapio, S.
C1  - 5751
C2  - 27456
SP  - 4710-4720
TI  - Formalin-fixed paraffin-embedded (FFPE) proteome analysis using gel-free and gel-based proteomics.
JO  - J. Proteome Res.
VL  - 9
IS  - 9
PB  - American Chemical Society
PY  - 2010
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - HER2-testing in breast and gastric cancers is mandatory for the treatment with trastuzumab. We hypothesized that imaging mass spectrometry (IMS) of breast cancers may be useful for generating a classifier that may determine HER2-status in other cancer entities irrespective of primary tumor site. A total of 107 breast (n = 48) and gastric (n = 59) cryo tissue samples was analyzed by IMS (HER2 was present in 29 cases). The obtained proteomic profiles were used to create HER2 prediction models using different classification algorithms. A breast cancer proteome derived classifier, with HER2 present in 15 cases, correctly predicted HER2-status in gastric cancers with a sensitivity of 65% and a specificity of 92%. To create a universal classifier for HER2-status, breast and nonbreast cancer samples were combined, which increased sensitivity to 78%, and specificity was 88%. Our proof of principle study provides evidence that HER2-status can be identified on a proteomic level across different cancer types suggesting that HER2 overexpression may constitute a unique molecular event independent of the tumor site. Furthermore, these results indicate that IMS may be useful for the determination of potential drugable targets, as it offers a quicker, cheaper, and more objective analysis than the standard HER2-testing procedures immunohistochemistry and fluorescence in situ hybridization.
AU  - Balluff, B.
AU  - Elsner, M.
AU  - Kowarsch, A.
AU  - Rauser, S.
AU  - Meding, S.
AU  - Schuhmacher, C.*
AU  - Feith, M.*
AU  - Herrmann, K.*
AU  - Röcken, C.*
AU  - Schmid, R.M.*
AU  - Höfler, H.
AU  - Walch, A.K.
AU  - Ebert, M.P.*
C1  - 2648
C2  - 27596
SP  - 6317-6322
TI  - Classification of HER2/neu status in gastric cancer using a breast-cancer derived proteome classifier.
JO  - J. Proteome Res.
VL  - 9
IS  - 12
PB  - American  Chemical Society
PY  - 2010
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Formalin fixation and paraffin embedding is the standard technique for preserving biological material for both storage and histological analysis. Although recent progress has been made in the molecular analysis of formalin-fixed, paraffin-embedded (FFPE) tissues, proteomic applications are a special challenge due to the cross-linking property of formalin. Here we present the results of a new formalin-free tissue fixative, PAXgene, and demonstrate successful extraction of nondegraded and immunoreactive protein for subsequent standard protein assays, such as Western blot analysis and reverse-phase protein arrays. High amounts of protein can be obtained from PAXgene-fixed, paraffin-embedded (PFPE) mouse liver and human spleen, breast, duodenum, and stomach tissues, similar to frozen material. By Western blot analysis, we found that the detection of membrane, cytoplasmic, nuclear, and phosphorylated protein from PAXgene-fixed human tissue samples was comparable to cryopreserved samples. Furthermore, the distribution of protein in PAXgene-fixed human tissue specimens is adequate for matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry for in situ proteomic analysis. Taken together, we demonstrate here that PAXgene has great potential to serve as a novel multimodal fixative for modern pathology, enabling extensive protein biomarker studies on clinical tissue samples.
AU  - Ergin, B.*
AU  - Meding, S.
AU  - Langer, R.*
AU  - Kap, M.*
AU  - Viertler, C.*
AU  - Schott, C.*
AU  - Ferch, U.*
AU  - Riegman, P.*
AU  - Zatloukal, K.*
AU  - Walch, A.K.
AU  - Becker, K.F.*
C1  - 2866
C2  - 27944
SP  - 5188-5196
TI  - Proteomic analysis of PAXgene-fixed tissues.
JO  - J. Proteome Res.
VL  - 9
IS  - 10
PB  - American Chemical Society
PY  - 2010
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Mutations in leucine-rich repeat kinase 2 (LRRK2) that increase its kinase activity associate with familial forms of Parkinson disease (PD). As phosphorylation determines the functional state of most protein kinases, we systematically mapped LRRK2 phosphorylation sites by mass spectrometry. Our analysis revealed a high degree of constitutive phosphorylation in a narrow serine-rich region preceding the LRR-domain. Allowing de novo autophosphorylation of purified LRRK2 in an in vitro autokinase assay prior to mass spectrometric analysis, we discovered multiple sites of autophosphorylation. Solely serine and threonine residues were found phosphorylated suggesting LRRK2 as a true serine threonine kinase. Autophosphorylation mainly targets the ROC GTPase domain and its clustering around the GTP binding pocket of ROC suggests cross-regulatory activity between kinase and Roc domain. In conclusion, the phosphoprotein LRRK2 functions as an autocatalytically active serine threonine kinase. Clustering of phosphosites within two discrete domains suggest that phosphorylation may regulate its biological functions in a yet unknown fashion.
AU  - Gloeckner, C.J.
AU  - Boldt, K.
AU  - von Zweydorf, F.
AU  - Helm, S.
AU  - Wiesent, L.
AU  - Sarioglu, H.
AU  - Ueffing, M.
C1  - 4755
C2  - 27767
SP  - 1738-1745
TI  - Phosphopeptide analysis reveals two discrete clusters of phosphorylation in the N-terminus and the Roc domain of the Parkinson-disease associated protein kinase LRRK2.
JO  - J. Proteome Res.
VL  - 9
IS  - 4
PB  - American Chemical Society
PY  - 2010
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Clinical laboratory testing for HER2 status in breast cancer tissues is critically important for therapeutic decision making. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for investigating proteins through the direct and morphology-driven analysis of tissue sections. We hypothesized that MALDI-IMS may determine HER2 status directly from breast cancer tissues. Breast cancer tissues (n = 48) predefined for HER2 status were subjected to MALDI-IMS, and protein profiles were obtained through direct analysis of tissue sections. Protein identification was performed by tissue microextraction and fractionation followed by top-down tandem mass spectrometry. A discovery and an independent validation set were used to predict HER2 status by applying proteomic classification algorithms. We found that specific protein/peptide expression changes strongly correlated with the HER2 overexpression. Among these, we identified m/z 8404 as cysteine-rich intestinal protein 1. The proteomic signature was able to accurately define HER2-positive from HER2-negative tissues, achieving high values for sensitivity of 83%, for specificity of 92%, and an overall accuracy of 89%. Our results underscore the potential of MALDI-IMS proteomic algorithms for morphology-driven tissue diagnostics such as HER2 testing and show that MALDI-IMS can reveal biologically significant molecular details from tissues which are not limited to traditional high-abundance proteins.
AU  - Rauser, S.
AU  - Marquardt, C.
AU  - Balluff, B.
AU  - Deininger, S.O.*
AU  - Albers, C.*
AU  - Belau, E.*
AU  - Hartmer, R.*
AU  - Suckau, D.*
AU  - Specht, K.*
AU  - Ebert, M.P.*
AU  - Schmitt, M.*
AU  - Aubele, M.
AU  - Höfler, H.
AU  - Walch, A.K.
C1  - 1382
C2  - 27156
SP  - 1854-1863
TI  - Classification of HER2 receptor status in breast cancer tissues by MALDI imaging mass spectrometry.
JO  - J. Proteome Res.
VL  - 9
IS  - 4
PB  - American Chemical Society
PY  - 2010
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - The spectrum of problems covered by proteomics studies range from the discovery of compartment specific cell proteomes to clinical applications, including the identification of diagnostic markers and monitoring the effects of drug treatments. In most cases, the ultimate results of a proteomics study are lists of proteins found to be present (or differentially present) at cell physiological conditions under study. Normally, the results are published directly in the article in one or several tables. In many cases, this type of information remains disseminated in hundreds of proteomics publications. We have developed a Web mining tool which allows the collection of this information by searching through full text papers and automatically selecting tables, which report a list of protein identifiers. By searching through major proteomics journals, we have collected approximately 800 independent studies published recently, which reported about 1000 different protein lists. On the basis of this data, we developed a computational tool PLIPS (Protein Lists Identified in Proteomics Studies). PLIPS accepts as input a list of protein/gene identifiers. With the use of statistical analyses, PLIPS infers recently published proteomics studies, which report protein lists that significantly intersect with a query list. PLIPS is a freely available Web-based tool (http://mips.helmholtz-muenchen.de/proj/plips).
AU  - Antonov, A.V.
AU  - Dietmann, S.
AU  - Wong, P.
AU  - Igor, R.
AU  - Mewes, H.-W.
C1  - 1354
C2  - 27009
SP  - 1193-1197
TI  - PLIPS, an automatically collected database of protein lists reported bMIPS: curated databasesy proteomics studies.
JO  - J. Proteome Res.
VL  - 8
IS  - 3
PB  - Amer Chemical Soc
PY  - 2009
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - We compared the protein expression pattern of triple-negative breast carcinomas (HER2-, ER-, PR-) versus those being positive for HER2 and negative for the hormone receptors (HER2+, ER-, PR-) by 2-D DIGE and mass spectrometry. We obtained differential expression patterns for several glycolytic enzymes (as for example MDH2, PGK1, TKT, Aldolase1), cytokeratins (CK7, 8, 9, 14, 17, 19), further structure proteins (vimentin, fibronectin, L-plastin), for NME1-NME2, lactoferrin, and members of the Annexin family. Western blot analysis and immunohistochemistry were conducted to verify the results. The identified marker proteins may advance a more detailed characterization of triple-negative breast cancers and may contribute to the development of better treatment strategies.
AU  - Schulz, D.M.
AU  - Böllner, C.
AU  - Thomas, G.*
AU  - Atkinson, M.J.
AU  - Esposito, I.
AU  - Höfler, H.
AU  - Aubele, M.
C1  - 2411
C2  - 26396
SP  - 3430-3438
TI  - Identification of differentially expressed proteins in triple-negative breast carcinomas using DIGE and mass spectrometry.
JO  - J. Proteome Res.
VL  - 8
IS  - 7
PB  - Amer Chemical Soc
PY  - 2009
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Environmental factors substantially contribute to the development of chronic intestinal inflammation in the genetically susceptible host. Nutritional components like iron may act as pro-oxidative mediators affecting inflammatory processes and cell stress mechanisms. To better characterize effects of dietary iron on epithelial cell responses under the pathological conditions of chronic intestinal inflammation, we characterized the protein expression profile (proteome) in primary intestinal epithelial cells (IEC) from iron-adequate and low-iron fed wild-type (WT) and TNF Delta ARE/WT mice. We performed all possible comparisons between the 4 groups according to genotype or diet. Histological analysis of iron-adequate fed TNF Delta ARE/WT mice (similar to 0.54 mg of iron/day) revealed severe ileal inflammation with a histopathology score of 8.3 +/- 0.91 (score range from 0-12). Interestingly, low-iron fed mice (similar to 0.03 mg of iron/day) were almost completely protected from the development of inflammatory tissue destruction (histopathology score of 2.30 +/- 0.73). In total, we identified 74 target proteins with significantly altered steady state expression levels in primary IEC using 2D-gel electrophoresis (2D SDS-PAGE) and peptide mass fingerprinting via MALDI-TOF mass spectrometry (MS). Interestingly, the overlap between the comparison of iron-adequate fed WT and TNF Delta ARE/WT mice (inflamed conditions) and the comparison between the iron-adequate and iron-low fed TNF Delta ARE/WT mice (absence of inflammation) revealed 4 contrarily regulated proteins including aconitase 2, catalase, intelectin 1 and fumarylacetoacetate hydrolase (FAH). These proteins are associated with energy homeostasis, host defense, oxidative and endoplasmic reticulum (ER) stress responses. In conclusion, the iron-low diet affected the epithelial cell proteome and inhibited the development of chronic intestinal inflammation, suggesting a critical role for nutritional factors in the pathogenesis of IBD.
AU  - Werner, T.*
AU  - Hoermannsperger, G.*
AU  - Schuemann, K.*
AU  - Hölzlwimmer, G.
AU  - Tsuji, S.*
AU  - Haller, D.*
C1  - 354
C2  - 26795
SP  - 3252-3264
TI  - Intestinal epithelial cell proteome from wild-type and TNF{Delta}ARE/WT mice: Effect of iron on the development of chronic ileitis.
JO  - J. Proteome Res.
VL  - 8
IS  - 7
PB  - Amer Chemical Soc
PY  - 2009
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Identification of biomarkers is of critical relevance toward improving diagnosis and therapy of autoimmune disorders. Serum markers are a desirable choice as sera are easily accessible and the development of assays for routine clinical detection prompts feasible. Autoimmune uveitis, a recurrent disease affecting the eye, is characterized by returning inflammatory attacks of the inner eye followed by variable periods of quiescent stages. Spontaneous equine recurrent uveitis (ERU) is the equine equivalent and serves as a model for the human disease. To identify potential biomarker candidates, we first systematically compared the proteomes of individual ERU cases with healthy controls by proteomic profiling using 2-D difference-gel-electrophoresis (2-D DIGE) followed by tandem mass spectrometry. A total of seven differentially expressed proteins were identified. Besides the upregulation of IgG and the significant lower expression of albumin, Antithrombin III, and Vitamin D binding protein, we found complement components C1q and C4, to be downregulated in uveitic state. Interestingly, Pigment epithelium-derived factor (PEDF), a marker already detected by 2DE differential proteome analysis in ERU target tissues, vitreous and retina, was found to be also significantly downregulated in sera. The lower expression of PEDF in sera of horses with uveitis could be verified in a cohort of 116 ERU cases and 115 healthy controls. Our findings of a significant lower PEDF expression in ERU cases also in the periphery of the eye proves PEDF as a promising uveitis biomarker.
AU  - Zipplies, J.K.*
AU  - Hauck, S.M.
AU  - Schoeffmann, S.
AU  - Amann, B.*
AU  - Stangassinger, M.*
AU  - Ueffing, M.
AU  - Deeg, C.A.*
C1  - 917
C2  - 26959
SP  - 992-998
TI  - Serum PEDF levels are decreased in a spontaneous animal model for human autoimmune uveitis.
JO  - J. Proteome Res.
VL  - 8
IS  - 2
PB  - Amer Chemical Soc
PY  - 2009
SN  - 1535-3893
ER  - 

TY  - JOUR
AB  - Spontaneous equine recurrent uveitis (ERU) is an incurable autoimmune disease affecting the eye. Although retinal-autoantigen specific T-helper 1 cells have been demonstrated to trigger disease progression and relapses, the molecular processes leading to retinal degeneration and consequent blindness remain unknown. To elucidate such processes, we studied changes in the total retinal proteome of ERU-diseased horses compared to healthy controls. Severe changes in the retinal proteome were found for several markers for blood-retinal barrier breakdown and whose emergence depended upon disease severity. Additionally, uveitic changes in the retina were accompanied by upregulation of aldose 1-epimerase, selenium-binding protein 1, alpha crystallin A chain, phosphatase 2A inhibitor (SET), and glial fibrillary acidic protein (GFAP), the latter indicating an involvement of retinal Mueller glial cells (RMG) in disease process. To confirm this, we screened for additional RMG-specific markers and could demonstrate that, in uveitic retinas, RMG concomitantly upregulate vimentin and GFAP and downregulate glutamine synthetase. These expression patterns suggest for an activated state of RMG, which further downregulate the expression of pigment epithelium-derived factor (PEDF) and begin expressing interferon-gamma, a pro-inflammatory cytokine typical for T-helper 1 cells. We thus propose that RMG may play a fatal role in uveitic disease progression by directly triggering inflammatory processes through the expression and secretion of interferon-gamma.
AU  - Hauck, S.M.
AU  - Schoeffmann, S.
AU  - Amann, B.*
AU  - Stangassinger, M.*
AU  - Gerhards, H.*
AU  - Ueffing, M.
AU  - Deeg , C.A.*
C1  - 5867
C2  - 24477
SP  - 2121-2131
TI  - Retinal Mueller Glial Cells Trigger the Hallmark Inflammatory Process in Autoimmune Uveitis.
JO  - J. Proteome Res.
VL  - 6
IS  - 6
PB  - ACS Publications
PY  - 2007
SN  - 1535-3893
ER  - 

TY  - JOUR
AU  - Alge, C.S.*
AU  - Hauck, S.M.
AU  - Priglinger, S.G.*
AU  - Kampik, A.*
AU  - Ueffing, M.
C1  - 2179
C2  - 23628
SP  - 862-878
TI  - Differential protein profiling of primary versus immortalized human RPE cells identifies expression patterns associated with cytoskeletal remodeling and cell survival.
JO  - J. Proteome Res.
VL  - 5
PY  - 2006
SN  - 1535-3893
ER  -