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1
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Huemer MT, Bauer A, Petrera A, Scholz M, Hauck SM, Drey M, Peters A, Thorand B. Proteomic profiling of low muscle and high fat mass: a machine learning approach in the KORA S4/FF4 study. J Cachexia Sarcopenia Muscle 2021; 12:1011-1023. [PMID: 34151535 PMCID: PMC8350207 DOI: 10.1002/jcsm.12733] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The coexistence of low muscle mass and high fat mass, two interrelated conditions strongly associated with declining health status, has been characterized by only a few protein biomarkers. High-throughput proteomics enable concurrent measurement of numerous proteins, facilitating the discovery of potentially new biomarkers. METHODS Data derived from the prospective population-based Cooperative Health Research in the Region of Augsburg S4/FF4 cohort study (median follow-up time: 13.5 years) included 1478 participants (756 men and 722 women) aged 55-74 years in the cross-sectional and 608 participants (315 men and 293 women) in the longitudinal analysis. Appendicular skeletal muscle mass (ASMM) and body fat mass index (BFMI) were determined through bioelectrical impedance analysis at baseline and follow-up. At baseline, 233 plasma proteins were measured using proximity extension assay. We implemented boosting with stability selection to enable false positives-controlled variable selection to identify new protein biomarkers of low muscle mass, high fat mass, and their combination. We evaluated prediction models developed based on group least absolute shrinkage and selection operator (lasso) with 100× bootstrapping by cross-validated area under the curve (AUC) to investigate if proteins increase the prediction accuracy on top of classical risk factors. RESULTS In the cross-sectional analysis, we identified kallikrein-6, C-C motif chemokine 28 (CCL28), and tissue factor pathway inhibitor as previously unknown biomarkers for muscle mass [association with low ASMM: odds ratio (OR) per 1-SD increase in log2 normalized protein expression values (95% confidence interval (CI)): 1.63 (1.37-1.95), 1.31 (1.14-1.51), 1.24 (1.06-1.45), respectively] and serine protease 27 for fat mass [association with high BFMI: OR (95% CI): 0.73 (0.61-0.86)]. CCL28 and metalloproteinase inhibitor 4 (TIMP4) constituted new biomarkers for the combination of low muscle and high fat mass [association with low ASMM combined with high BFMI: OR (95% CI): 1.32 (1.08-1.61), 1.28 (1.03-1.59), respectively]. Including protein biomarkers selected in ≥90% of group lasso bootstrap iterations on top of classical risk factors improved the performance of models predicting low ASMM, high BFMI, and their combination [delta AUC (95% CI): 0.16 (0.13-0.20), 0.22 (0.18-0.25), 0.12 (0.08-0.17), respectively]. In the longitudinal analysis, N-terminal prohormone brain natriuretic peptide (NT-proBNP) was the only protein selected for loss in ASMM and loss in ASMM combined with gain in BFMI over 14 years [OR (95% CI): 1.40 (1.10-1.77), 1.60 (1.15-2.24), respectively]. CONCLUSIONS Proteomic profiling revealed CCL28 and TIMP4 as new biomarkers of low muscle mass combined with high fat mass and NT-proBNP as a key biomarker of loss in muscle mass combined with gain in fat mass. Proteomics enable us to accelerate biomarker discoveries in muscle research.
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Affiliation(s)
- Marie-Theres Huemer
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Alina Bauer
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Agnese Petrera
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), Universität Leipzig, Leipzig, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Drey
- Medizinische Klinik und Poliklinik IV, Schwerpunkt Akutgeriatrie, Klinikum der Universität München (LMU), Munich, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,Chair of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
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2
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Adamo A, Brandi J, Caligola S, Delfino P, Bazzoni R, Carusone R, Cecconi D, Giugno R, Manfredi M, Robotti E, Marengo E, Bassi G, Takam Kamga P, Dal Collo G, Gatti A, Mercuri A, Arigoni M, Olivero M, Calogero RA, Krampera M. Extracellular Vesicles Mediate Mesenchymal Stromal Cell-Dependent Regulation of B Cell PI3K-AKT Signaling Pathway and Actin Cytoskeleton. Front Immunol 2019; 10:446. [PMID: 30915084 PMCID: PMC6423067 DOI: 10.3389/fimmu.2019.00446] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are adult, multipotent cells of mesodermal origin representing the progenitors of all stromal tissues. MSCs possess significant and broad immunomodulatory functions affecting both adaptive and innate immune responses once MSCs are primed by the inflammatory microenvironment. Recently, the role of extracellular vesicles (EVs) in mediating the therapeutic effects of MSCs has been recognized. Nevertheless, the molecular mechanisms responsible for the immunomodulatory properties of MSC-derived EVs (MSC-EVs) are still poorly characterized. Therefore, we carried out a molecular characterization of MSC-EV content by high-throughput approaches. We analyzed miRNA and protein expression profile in cellular and vesicular compartments both in normal and inflammatory conditions. We found several proteins and miRNAs involved in immunological processes, such as MOES, LG3BP, PTX3, and S10A6 proteins, miR-155-5p, and miR-497-5p. Different in silico approaches were also performed to correlate miRNA and protein expression profile and then to evaluate the putative molecules or pathways involved in immunoregulatory properties mediated by MSC-EVs. PI3K-AKT signaling pathway and the regulation of actin cytoskeleton were identified and functionally validated in vitro as key mediators of MSC/B cell communication mediated by MSC-EVs. In conclusion, we identified different molecules and pathways responsible for immunoregulatory properties mediated by MSC-EVs, thus identifying novel therapeutic targets as safer and more useful alternatives to cell or EV-based therapeutic approaches.
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Affiliation(s)
- Annalisa Adamo
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Jessica Brandi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Simone Caligola
- Department of Computer Science, University of Verona, Verona, Italy
| | - Pietro Delfino
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Riccardo Bazzoni
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Roberta Carusone
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Daniela Cecconi
- Proteomics and Mass Spectrometry Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Marcello Manfredi
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), Novara, Italy
| | - Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), Novara, Italy
| | - Giulio Bassi
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Paul Takam Kamga
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Giada Dal Collo
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Alessandro Gatti
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Angela Mercuri
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | | | - Raffaele A Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Mauro Krampera
- Stem Cell Research Laboratory, Section of Hematology, Department of Medicine, University of Verona, Verona, Italy
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Manfredi M, Chiariello C, Conte E, Castagna A, Robotti E, Gosetti F, Patrone M, Martinelli N, Bassi A, Cecconi D, Marengo E, Olivieri O. Plasma Proteome Profiles of Stable CAD Patients Stratified According to Total Apo C‐III Levels. Proteomics Clin Appl 2018; 13:e1800023. [DOI: 10.1002/prca.201800023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/30/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Marcello Manfredi
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
- ISALIT S.r.l. Via Canobia 4/6 28100 Novara Italy
| | - Carmela Chiariello
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | | | - Annalisa Castagna
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | - Elisa Robotti
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
- ISALIT S.r.l. Via Canobia 4/6 28100 Novara Italy
| | - Fabio Gosetti
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
| | - Mauro Patrone
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
| | - Nicola Martinelli
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | - Antonella Bassi
- Laboratory of Clinical Chemistry and HematologyUniversity Hospital of Verona P.le L.A. Scuro 10 37134 Verona Italy
| | - Daniela Cecconi
- Department of BiotechnologyProteomics and Mass Spectrometry LaboratoryUniversity of Verona Strada le grazie 15 37134 Verona Italy
| | - Emilio Marengo
- Department of Sciences and Technological InnovationUniversity of Piemonte Orientale Viale T. Michel 11 15121 Alessandria Italy
| | - Oliviero Olivieri
- Department of MedicineUnit of Internal MedicineUniversity of Verona P.le L.A. Scuro 10 37134 Verona Italy
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Moiseeva TN, Gamper AM, Hood BL, Conrads TP, Bakkenist CJ. Human DNA polymerase ε is phosphorylated at serine-1940 after DNA damage and interacts with the iron-sulfur complex chaperones CIAO1 and MMS19. DNA Repair (Amst) 2016; 43:9-17. [PMID: 27235625 DOI: 10.1016/j.dnarep.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/12/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
We describe a dynamic phosphorylation on serine-1940 of the catalytic subunit of human Pol ε, POLE1, following DNA damage. We also describe novel interactions between POLE1 and the iron-sulfur cluster assembly complex CIA proteins CIAO1 and MMS19. We show that serine-1940 is essential for the interaction between POLE1 and MMS19, but not POLE1 and CIAO1. No defect in either proliferation or survival was identified when POLE1 serine-1940 was mutated to alanine in human cells, even following treatment with DNA damaging agents. We conclude that serine-1940 phosphorylation and the interaction between serine-1940 and MMS19 are not essential functions in the C terminal domain of the catalytic subunit of DNA polymerase ε.
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Affiliation(s)
- Tatiana N Moiseeva
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863, USA
| | - Armin M Gamper
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863, USA; Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6 G 1Z2, Canada
| | - Brian L Hood
- Women's Health Integrated Research Center at Inova Health System, Department of Defense Gynecologic Cancer Center of Excellence, Annandale, VA 22003, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center at Inova Health System, Department of Defense Gynecologic Cancer Center of Excellence, Annandale, VA 22003, USA
| | - Christopher J Bakkenist
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863, USA.
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5
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Digilio G, Sforzini S, Cassino C, Robotti E, Oliveri C, Marengo E, Musso D, Osella D, Viarengo A. Haemolymph from Mytilus galloprovincialis: Response to copper and temperature challenges studied by (1)H-NMR metabonomics. Comp Biochem Physiol C Toxicol Pharmacol 2016; 183-184:61-71. [PMID: 26899427 DOI: 10.1016/j.cbpc.2016.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/01/2016] [Accepted: 02/15/2016] [Indexed: 01/18/2023]
Abstract
Numerous studies on molluscs have been carried out to clarify the physiological roles of haemolymph serum proteins and haemocytes. However, little is known about the presence and functional role of the serum metabolites. In this study, Nuclear Magnetic Resonance (NMR) was used to assess whether changes of the metabolic profile of Mytilus galloprovincialis haemolymph may reflect alterations of the physiological status of the organisms due to environmental stressors, namely copper and temperature. Mussel haemolymph was taken from the posterior adductor muscle after a 4-day exposure to ambient (16 °C) or high temperature (24 °C) and in the absence or presence (5 μg/L, 20 μg/L, or 40 μg/L) of sublethal copper (Cu(2+)). The total glutathione (GSH) concentration in the haemolymph of both control and treated mussels was minimal, indicating the absence of significant contaminations by muscle intracellular metabolites due to the sampling procedure. In the (1)H-NMR spectrum of haemolymph, 27 metabolites were identified unambiguously. The separate and combined effects of exposure to copper and temperature on the haemolymph metabolic profile were assessed by Principal Component Analysis (PCA) and Ranking-PCA multivariate analysis. Changes of the metabolomic profile due to copper exposure at 16 °C became detectable at a dose of 20 μg/L copper. Alanine, lysine, serine, glutamine, glycogen, glucose and protein aliphatics played a major role in the classification of the metabolic changes according to the level of copper exposition. High temperature (24 °C) and high copper levels caused a coherent increase of a common set of metabolites (mostly glucose, serine, and lysine), indicating that the metabolic impairment due to high temperature is enforced by the presence of copper. Overall, the results demonstrate that, as for human blood plasma, the analysis of haemolymph metabolites represents a promising tool for the diagnosis of pollutant-induced stress syndrome in marine mussels.
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Affiliation(s)
- Giuseppe Digilio
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Susanna Sforzini
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Claudio Cassino
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Elisa Robotti
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Caterina Oliveri
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Emilio Marengo
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Davide Musso
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Domenico Osella
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy
| | - Aldo Viarengo
- Department of Sciences and Technological Innovation (DiSIT), University of Piemonte Orientale "Amedeo Avogadro", Viale T. Michel 11, 15121 Alessandria, Italy.
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6
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Robotti E, Marengo E. Chemometric Multivariate Tools for Candidate Biomarker Identification: LDA, PLS-DA, SIMCA, Ranking-PCA. Methods Mol Biol 2016; 1384:237-267. [PMID: 26611419 DOI: 10.1007/978-1-4939-3255-9_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
2-D gel electrophoresis usually provides complex maps characterized by a low reproducibility: this hampers the use of spot volume data for the identification of reliable biomarkers. Under these circumstances, effective and robust methods for the comparison and classification of 2-D maps are fundamental for the identification of an exhaustive panel of candidate biomarkers. Multivariate methods are the most suitable since they take into consideration the relationships between the variables, i.e., effects of synergy and antagonism between the spots. Here the most common multivariate methods used in spot volume datasets analysis are presented. The methods are applied on a sample dataset to prove their effectiveness.
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Affiliation(s)
- Elisa Robotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121, Alessandria, Italy.
| | - Emilio Marengo
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Viale Michel 11, 15121, Alessandria, Italy
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7
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Han Y, Zhou M, Wang L, Ying X, Peng J, Jiang M, Bai G, Luo G. Comparative evaluation of different cultivars of Flos Chrysanthemi by an anti-inflammatory-based NF-κB reporter gene assay coupled to UPLC-Q/TOF MS with PCA and ANN. JOURNAL OF ETHNOPHARMACOLOGY 2015; 174:387-395. [PMID: 26320691 DOI: 10.1016/j.jep.2015.08.044] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/14/2015] [Accepted: 08/26/2015] [Indexed: 06/04/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Flos Chrysanthemi (FC), a commonly used traditional Chinese medicine, has five major cultivars ("Boju", "Chuju", "Gongju", "Hangbaiju" and "Huaiju") from different sources. However, the active constituents of these cultivars have not been studied or characterized with respect to their bioactivity, which is a serious problem when considering quality and safety. AIM OF THE STUDY To evaluate the differences among the five cultivars of FC, and to establish a method for the standardization and quality control of FC related to its bioactivity. MATERIALS AND METHODS In this study, the different ingredients in five cultivars of FC were identified by UPLC-Q/TOF and PCA, and the anti-inflammatory ingredients of FC were predicted and screened by artificial neural network (ANN) and an NF-κB luciferase reporter gene assay system. Using this comprehensive method, we successfully screened the anti-inflammatory markers of different cultivars of FC. RESULTS Nineteen marker ingredients were confirmed to contribute strongly to the cluster, and eleven compounds in the five cultivars of FC were found to exert potential anti-inflammatory effects. Among these compounds, the NF-κB inhibitor activity of apigenin-7-O-6″-malonyl-glucoside, luteolin-7-O-rutinoside, quercetin-7-O-galactoside, quercetin-3-O-glucoside, apigenin-7-O-rutinoside and apigenin-7-O-glucoside were first reported here. Chlorogenic acid, luteolin-7-O-glucoside, 3,5-dicaffeoylquinic acid and luteolin were confirmed to be the most important anti-inflammatory marker ingredients useful for the quality control of FC. CONCLUSIONS The proposed efficient and systematic method is helpful for the standardization and quality control of FC. Moreover, this comprehensive strategy may prove to be a powerful technique for the rapid establishment of quality control procedures related to bioactivity for other herbal samples and foods.
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Affiliation(s)
- Yanqi Han
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin 300071, People's Republic of China
| | - Mengge Zhou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin 300071, People's Republic of China
| | - Liqiang Wang
- Tianjin Entry-Exit Inspection and Quarantine Bureau, Tianjin 300461, People's Republic of China
| | - Xuhui Ying
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin 300071, People's Republic of China
| | - Jiamin Peng
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin 300071, People's Republic of China
| | - Min Jiang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin 300071, People's Republic of China.
| | - Gang Bai
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin 300071, People's Republic of China
| | - Guoan Luo
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, College of Pharmacy, Nankai University, Tianjin 300071, People's Republic of China; Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China
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8
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Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S. Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients. BMC Genomics 2015; 16:876. [PMID: 26510930 PMCID: PMC4625854 DOI: 10.1186/s12864-015-2058-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/02/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD. METHODS Changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls ("Discovery set") were analyzed by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. Data analysis was performed by applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays. Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes. The expressions of selected genes were validated using RT-qPCR and samples from an independent cohort of 12 patients and controls ("Validation set"). RESULTS Gene expression profiling of blood samples discriminates PD patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts as CBX5, TCF3, MAN1C1 and DOCK10 were validated by RT-qPCR. CONCLUSIONS Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.
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Affiliation(s)
- Raffaella Calligaris
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Mihaela Banica
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Paola Roncaglia
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. .,Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), CB10 1SD Hinxton, Cambridge, UK.
| | - Elisa Robotti
- Department of Environmental and Life Sciences, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy.
| | - Sara Finaurini
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Christina Vlachouli
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Lucia Antonutti
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Francesco Iorio
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy. .,Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), CB10 1SD Hinxton, Cambridge, UK.
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy.
| | - Tatiana Cattaruzza
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Andrea Ceiner
- ITALTBS S.p.A., AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.
| | - Dejan Lazarevic
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. .,CBM Scrl - Consorzio per il Centro di Biomedicina Molecolare, Area Science Park, S.S.14, km 163.5, Basovizza, 34149, Trieste, Italy.
| | - Alberto Cucca
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Nicola Pangher
- ITALTBS S.p.A., AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.
| | - Emilio Marengo
- Department of Environmental and Life Sciences, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy.
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy. .,Department Computer Science & Systems, School of Engineering, University of Naples "Federico II", via Claudio 21, 80125, Naples, Italy.
| | - Gilberto Pizzolato
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Stefano Gustincich
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
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Hood BL, Liu B, Alkhas A, Shoji Y, Challa R, Wang G, Ferguson S, Oliver J, Mitchell D, Bateman NW, Zahn CM, Hamilton CA, Payson M, Lessey B, Fazleabas AT, Maxwell GL, Conrads TP, Risinger JI. Proteomics of the Human Endometrial Glandular Epithelium and Stroma from the Proliferative and Secretory Phases of the Menstrual Cycle1. Biol Reprod 2015; 92:106. [DOI: 10.1095/biolreprod.114.127217] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/16/2015] [Indexed: 01/04/2023] Open
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10
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Marengo E, Robotti E. Biomarkers for pancreatic cancer: Recent achievements in proteomics and genomics through classical and multivariate statistical methods. World J Gastroenterol 2014; 20:13325-13342. [PMID: 25309068 PMCID: PMC4188889 DOI: 10.3748/wjg.v20.i37.13325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 06/04/2014] [Accepted: 06/26/2014] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is one of the most aggressive and lethal neoplastic diseases. A valid alternative to the usual invasive diagnostic tools would certainly be the determination of biomarkers in peripheral fluids to provide less invasive tools for early diagnosis. Nowadays, biomarkers are generally investigated mainly in peripheral blood and tissues through high-throughput omics techniques comparing control vs pathological samples. The results can be evaluated by two main strategies: (1) classical methods in which the identification of significant biomarkers is accomplished by monovariate statistical tests where each biomarker is considered as independent from the others; and (2) multivariate methods, taking into consideration the correlations existing among the biomarkers themselves. This last approach is very powerful since it allows the identification of pools of biomarkers with diagnostic and prognostic performances which are superior to single markers in terms of sensitivity, specificity and robustness. Multivariate techniques are usually applied with variable selection procedures to provide a restricted set of biomarkers with the best predictive ability; however, standard selection methods are usually aimed at the identification of the smallest set of variables with the best predictive ability and exhaustivity is usually neglected. The exhaustive search for biomarkers is instead an important alternative to standard variable selection since it can provide information about the etiology of the pathology by producing a comprehensive set of markers. In this review, the most recent applications of the omics techniques (proteomics, genomics and metabolomics) to the identification of exploratory biomarkers for PC will be presented with particular regard to the statistical methods adopted for their identification. The basic theory related to classical and multivariate methods for identification of biomarkers is presented and then, the most recent applications in this field are discussed.
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11
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Dissecting the transcriptional phenotype of ribosomal protein deficiency: implications for Diamond-Blackfan Anemia. Gene 2014; 545:282-9. [PMID: 24835311 PMCID: PMC4058751 DOI: 10.1016/j.gene.2014.04.077] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 04/04/2014] [Accepted: 04/29/2014] [Indexed: 11/26/2022]
Abstract
Defects in genes encoding ribosomal proteins cause Diamond Blackfan Anemia (DBA), a red cell aplasia often associated with physical abnormalities. Other bone marrow failure syndromes have been attributed to defects in ribosomal components but the link between erythropoiesis and the ribosome remains to be fully defined. Several lines of evidence suggest that defects in ribosome synthesis lead to “ribosomal stress” with p53 activation and either cell cycle arrest or induction of apoptosis. Pathways independent of p53 have also been proposed to play a role in DBA pathogenesis. We took an unbiased approach to identify p53-independent pathways activated by defects in ribosome synthesis by analyzing global gene expression in various cellular models of DBA. Ranking-Principal Component Analysis (Ranking-PCA) was applied to the identified datasets to determine whether there are common sets of genes whose expression is altered in these different cellular models. We observed consistent changes in the expression of genes involved in cellular amino acid metabolic process, negative regulation of cell proliferation and cell redox homeostasis. These data indicate that cells respond to defects in ribosome synthesis by changing the level of expression of a limited subset of genes involved in critical cellular processes. Moreover, our data support a role for p53-independent pathways in the pathophysiology of DBA.
Ribosomopathies such as DBA are caused by ribosome dysfunction that activates p53. p53-independent pathways may suggest possible treatments for DBA. Expression analysis was performed in three p53-null models of DBA. Genes involved in apoptosis and cell redox homeostasis were especially affected. DBA is due to cumulative effects of p53-dependent and independent pathways.
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12
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Identification of candidate circulating cisplatin-resistant biomarkers from epithelial ovarian carcinoma cell secretomes. Br J Cancer 2013; 110:123-32. [PMID: 24178762 PMCID: PMC3887292 DOI: 10.1038/bjc.2013.687] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 12/12/2022] Open
Abstract
Background: The majority of patients diagnosed with advanced epithelial ovarian carcinoma (EOC) relapse with resistant disease, and there are no biomarkers that possess clinical utility to identify or monitor these patients. This study aimed to identify secreted proteins (‘secretome') collected from human EOC cell lines that differ in their inherent platinum sensitivity. Methods: Secreted proteins collected from conditioned medium from ovarian cancer cell lines that vary in their sensitivity to cisplatin were digested with trypsin and analysed by liquid chromatography-tandem mass spectrometry for peptide identification. Results: Of the 1688 proteins identified, 16 possessed significant differential abundances (P<0.05) between the platinum-resistant and -sensitive cell lines. A number of these were verified by immunoblot, including COL11A1, which was also found to be associated with worse progression-free survival (PFS; N=723) and overall survival (OS; N=1183) as assessed from publicly available transcript expression data from ovarian cancer tumour specimens. Conclusion: Secretome proteomics of EOC cells resulted in the identification of a novel candidate biomarker, COL11A1. The expression level of COL11A1 correlates to worse PFS and OS, and is predicted to reside in peripheral circulation making this an attractive candidate for validation in sera as a biomarker of cisplatin resistance and poor outcome.
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Kan AA, de Jager W, de Wit M, Heijnen C, van Zuiden M, Ferrier C, van Rijen P, Gosselaar P, Hessel E, van Nieuwenhuizen O, de Graan PNE. Protein expression profiling of inflammatory mediators in human temporal lobe epilepsy reveals co-activation of multiple chemokines and cytokines. J Neuroinflammation 2012; 9:207. [PMID: 22935090 PMCID: PMC3489559 DOI: 10.1186/1742-2094-9-207] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 07/30/2012] [Indexed: 11/25/2022] Open
Abstract
Mesial temporal lobe epilepsy (mTLE) is a chronic and often treatment-refractory brain disorder characterized by recurrent seizures originating from the hippocampus. The pathogenic mechanisms underlying mTLE remain largely unknown. Recent clinical and experimental evidence supports a role of various inflammatory mediators in mTLE. Here, we performed protein expression profiling of 40 inflammatory mediators in surgical resection material from mTLE patients with and without hippocampal sclerosis, and autopsy controls using a multiplex bead-based immunoassay. In mTLE patients we identified 21 upregulated inflammatory mediators, including 10 cytokines and 7 chemokines. Many of these upregulated mediators have not previously been implicated in mTLE (for example, CCL22, IL-7 and IL-25). Comparing the three patient groups, two main hippocampal expression patterns could be distinguished, pattern I (for example, IL-10 and IL-25) showing increased expression in mTLE + HS patients compared to mTLE-HS and controls, and pattern II (for example, CCL4 and IL-7) showing increased expression in both mTLE groups compared to controls. Upregulation of a subset of inflammatory mediators (for example, IL-25 and IL-7) could not only be detected in the hippocampus of mTLE patients, but also in the neocortex. Principle component analysis was used to cluster the inflammatory mediators into several components. Follow-up analyses of the identified components revealed that the three patient groups could be discriminated based on their unique expression profiles. Immunocytochemistry showed that IL-25 IR (pattern I) and CCL4 IR (pattern II) were localized in astrocytes and microglia, whereas IL-25 IR was also detected in neurons. Our data shows co-activation of multiple inflammatory mediators in hippocampus and neocortex of mTLE patients, indicating activation of multiple pro- and anti-epileptogenic immune pathways in this disease.
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Affiliation(s)
- Anne A Kan
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Wilco de Jager
- Department of Pediatric Immunology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
| | - Marina de Wit
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Cobi Heijnen
- Laboratory of Neuroimmunology and Developmental Origins of Disease, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Mirjam van Zuiden
- Laboratory of Neuroimmunology and Developmental Origins of Disease, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Cyrill Ferrier
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
| | - Peter van Rijen
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
| | - Peter Gosselaar
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
| | - Ellen Hessel
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Onno van Nieuwenhuizen
- Department of Child Neurology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
| | - Pierre N E de Graan
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
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14
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Polati R, Menini M, Robotti E, Millioni R, Marengo E, Novelli E, Balzan S, Cecconi D. Proteomic changes involved in tenderization of bovine Longissimus dorsi muscle during prolonged ageing. Food Chem 2012; 135:2052-69. [PMID: 22953957 DOI: 10.1016/j.foodchem.2012.06.093] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 06/05/2012] [Accepted: 06/25/2012] [Indexed: 02/07/2023]
Abstract
To study proteomic changes involved in tenderization of bovine Longissimus dorsi four Charolaise heifers and four Charolaise bull's muscles were sampled at slaughter after early and long ageing (2-4°C for 12 and 26days respectively). Descriptive sensory evaluation of samples were performed and their tenderness evaluated by Warner-Bratzler shear force test. Protein composition of fresh muscle and of meat aged was analysed by cartesian and polar 2-D electrophoresis. Student's t-test and Ranking-PCA analyses were performed to detect proteomic modulation, and the selected protein spots were identified by nano-HPLC-Chip MS/MS. This research has demonstrated that there are no differences between proteomic patterns of male and females Longissimus dorsi muscle, and that the extension of ageing beyond 12days, did not brings any concrete advantage in terms of sensory quality. Furthermore, the data presented here demonstrated that meat maturation caused changes of the abundance of proteins involved in metabolic, structural, and stress related processes.
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Affiliation(s)
- Rita Polati
- Department of Biotechnology, Proteomics and Mass Spectrometry Laboratory, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
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Pierce KM, Mohler RE. A Review of Chemometrics Applied to Comprehensive Two-dimensional Separations from 2008–2010. SEPARATION AND PURIFICATION REVIEWS 2012. [DOI: 10.1080/15422119.2011.591868] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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16
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[Application of capillary electrophoresis in analysis of disease specific proteins]. Se Pu 2011; 29:298-302. [PMID: 21770237 DOI: 10.3724/sp.j.1123.2011.00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
One of the most urgent things in life science is to find out special proteins related to human diseases. Capillary electrophoresis (CE) shows many advantages in protein analysis, such as high separation efficiency, high speed, low cost, etc. Furthermore, there are many different separation modes and multifarious detectors can be chosen in CE for the analysis of different samples. In this paper, the applications of CE in the analysis of specific proteins, which might associate with some serious diseases, such as tumor, neurodegenerative disease and transfusion transmitted infections, are summarized.
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Robotti E, Demartini M, Gosetti F, Calabrese G, Marengo E. Development of a classification and ranking method for the identification of possible biomarkers in two-dimensional gel-electrophoresis based on principal component analysis and variable selection procedures. MOLECULAR BIOSYSTEMS 2011; 7:677-86. [PMID: 21286649 DOI: 10.1039/c0mb00124d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The identification of biomarkers is one of the leading research areas in proteomics. When biomarkers have to be searched for in spot volume datasets produced by 2D gel-electrophoresis, problems may arise related to the large number of spots present in each map and the small number of samples available in each class (control/pathological). In such cases multivariate methods are usually exploited together with variable selection procedures, to provide a set of possible biomarkers: they are however usually aimed to the selection of the smallest set of variables (spots) providing the best performances in prediction. This approach seems not to be suitable for the identification of potential biomarkers since in this case all the possible candidate biomarkers have to be identified to provide a general picture of the "pathological state": in this case exhaustivity has to be preferred to provide a complete understanding of the mechanisms underlying the pathology. We propose here a ranking and classification method, "Ranking-PCA", based on Principal Component Analysis and variable selection in forward search: the method selects one variable at a time as the one providing the best separation of the two classes investigated in the space given by the relevant PCs. The method was applied to an artificial dataset and a real case-study: Ranking-PCA exhaustively identified the potential biomarkers and provided reliable and robust results.
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Affiliation(s)
- Elisa Robotti
- Department of Environmental and Life Sciences, University of Eastern Piedmont, Viale T. Michel 11, 15121 Alessandria, Italy
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18
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Bateman NW, Sun M, Bhargava R, Hood BL, Darfler MM, Kovatich AJ, Hooke JA, Krizman DB, Conrads TP. Differential proteomic analysis of late-stage and recurrent breast cancer from formalin-fixed paraffin-embedded tissues. J Proteome Res 2011; 10:1323-32. [PMID: 21155598 DOI: 10.1021/pr101073s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The heterogeneity of breast cancer requires the discovery of more incisive molecular tools that better define disease progression and prognosis. Proteomic analysis of homogeneous tumor cell populations derived by laser microdissection from formalin-fixed, paraffin-embedded (FFPE) tissues has proven to be a robust strategy for conducting retrospective cancer biomarker investigations. We describe an MS-based analysis of laser microdissected cancerous epithelial cells derived from twenty-five breast cancer patients at defined clinical disease stages with the goal of identifying protein abundance characteristics indicative of disease progression and recurrence. Comparative analysis of stage 0 and stage III patients revealed 113 proteins that significantly differentiated these groups and included known factors associated with disease pathogenesis, such as CDH1 and CTNNB1, as well as those previously implicated in breast cancer, such as TSP-1. Similar analyses of patients presenting with stage II disease that did or did not exhibit recurrence two years postdiagnosis revealed 42 proteins that significantly differentiated these subgroups and included IRS-1 and PARK7. These data provide evidence supporting the utility of FFPE tissues for functional proteomic analyses and protein biomarker discovery and yielded protein candidates indicative of disease stage and recurrence in breast cancer that warrant further investigation for diagnostic utility and biological relevance.
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Affiliation(s)
- Nicholas W Bateman
- Department of Pharmacology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Bateman NW, Sun M, Hood BL, Flint MS, Conrads TP. Defining central themes in breast cancer biology by differential proteomics: conserved regulation of cell spreading and focal adhesion kinase. J Proteome Res 2010; 9:5311-24. [PMID: 20681588 DOI: 10.1021/pr100580e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Breast cancer is a highly heterogeneous disease, an observation that underscores the importance of elucidating conserved molecular characteristics, such as gene and protein expression, across breast cancer cell types toward providing a greater understanding of context-specific features central to this disease. Motivated by the goal of defining central biological themes across breast cancer cell subtypes, we conducted a global proteomic analysis of three breast cancer cell lines, MCF7, SK-BR-3, and MDA-MB-231, and compared these to a model of nontransformed mammary cells (MCF10A). Our results demonstrate modulation of proteins localized to the extracellular matrix, plasma membrane, and nucleus, along with coordinate decreases in proteins that regulate "cell spreading," a cellular event previously shown to be dysregulated in transformed cells. Protein interaction network analysis revealed the clustering of focal adhesion kinase (FAK), a fundamental regulator of cell spreading, with several proteins identified as mutually, differentially abundant across breast cancer cell lines that impact expression and activity of FAK, such as neprilysin and keratin 19. These analyses provide insights into conservation of protein expression across breast cancer cell subtypes, a subset of which warrants further investigation for their roles in the regulation of cell spreading and FAK in breast cancer.
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Affiliation(s)
- Nicholas W Bateman
- Department of Pharmacology & Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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