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Brozek-Pluska B, Kopec M, Surmacki J, Abramczyk H. Raman microspectroscopy of noncancerous and cancerous human breast tissues. Identification and phase transitions of linoleic and oleic acids by Raman low-temperature studies. Analyst 2015; 140:2134-43. [PMID: 25722994 DOI: 10.1039/c4an01877j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present the results of Raman studies in the temperature range of 293-77 K on vibrational properties of linoleic and oleic acids and Raman microspectroscopy of human breast tissues at room temperature. Our results confirmed the significant role of unsaturated fatty acids in differentiation of noncancerous and cancerous breast tissues and the role of vibrational spectroscopy in phase transition identification. We have found that vibrational properties are very sensitive indicators to specify phases and phase transitions typical of unsaturated fatty acids at the molecular level. Using Raman spectroscopy we have identified high-temperature, middle-temperature and low-temperature phases of linoleic acid. Results obtained for linoleic acid were compared with parameters characteristic of α and γ phases of oleic acid - the parent compound of polyunsaturated fatty acids.
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Affiliation(s)
- Beata Brozek-Pluska
- Lodz University of Technology, Institute of Applied Radiation Chemistry, Laboratory of Laser Molecular Spectroscopy, Wroblewskiego 15, 93-590 Lodz, Poland.
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Combined regulation of mTORC1 and lysosomal acidification by GSK-3 suppresses autophagy and contributes to cancer cell growth. Oncogene 2014; 34:4613-23. [PMID: 25500539 DOI: 10.1038/onc.2014.390] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/10/2014] [Accepted: 10/16/2014] [Indexed: 12/11/2022]
Abstract
There is controversy over the role of glycogen synthase kinase-3 (GSK-3) in cancer progression. Recent work has implicated GSK-3 in the regulation of mammalian target of rapamycin (mTOR), a known player in malignant transformation. Autophagy, a self-degradation pathway, is inhibited by mTOR and is tightly associated with cell survival and tumor growth. Here we show that GSK-3 suppresses autophagy via mTOR complex-1 (mTORC1) and lysosomal regulation. We show that overexpression of GSK-3 isoforms (GSK-3α and GSK-3β) activated mTORC1 and suppressed autophagy in MCF-7 human breast cancer cells as indicated by reduced beclin-1 levels and upregulation of sequestosome 1 (p62/SQSTM1). Further, overexpression of GSK-3 increased the number of autophagosomes and inhibited autophagic flux. This activity was directly related to reduced lysosomal acidification triggered by GSK-3 (in which GSK-3β has a stronger impact). We found that lysosomal acidification is reduced in MCF-7 cells that also exhibit increased levels of autophagosomes and p62/SQSTM1 and increased activity of mTORC1. Subsequently, treating cells with GSK-3 inhibitors restored lysosomal acidification, enhanced autophagic flux and inhibited mTORC1. Furthermore, GSK-3 inhibitors inhibited cell proliferation. We provide evidence that GSK3-mediated mTORC1 activity and GSK-3-mediated lysosomal acidification occur via distinct pathways, yet both mTORC1 and lysosomes control cell growth. Finally, we show that GSK-3-reduced lysosomal acidification inhibits endocytic clearance as demonstrated by reduced endocytic degradation of the epidermal growth factor receptor. Taken together, our study places GSK-3 as a key regulator coordinating cellular homeostasis. GSK-3 inhibitors may be useful in targeting mTORC1 and lysosomal acidification for cancer therapy.
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Nagano K, Akpan A, Warnasuriya G, Corless S, Totty N, Yang A, Stein R, Zvelebil M, Stensballe A, Burlingame A, Waterfield M, Cramer R, Timms JF, Naaby-Hansen S. Functional proteomic analysis of long-term growth factor stimulation and receptor tyrosine kinase coactivation in Swiss 3T3 fibroblasts. Mol Cell Proteomics 2012; 11:1690-708. [PMID: 22956732 DOI: 10.1074/mcp.m112.019778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Swiss 3T3 fibroblasts, long-term stimulation with PDGF, but not insulin-like growth factor 1 (IGF-1) or EGF, results in the establishment of an elongated migratory phenotype, characterized by the formation of retractile dendritic protrusions and absence of actin stress fibers and focal adhesion complexes. To identify receptor tyrosine kinase-specific reorganization of the Swiss 3T3 proteome during phenotypic differentiation, we compared changes in the pattern of protein synthesis and phosphorylation during long-term exposure to PDGF, IGF-1, EGF, and their combinations using 2DE-based proteomics after (35)S- and (33)P-metabolic labeling. One hundred and five differentially regulated proteins were identified by mass spectrometry and some of these extensively validated. PDGF stimulation produced the highest overall rate of protein synthesis at any given time and induced the most sustained phospho-signaling. Simultaneous activation with two or three of the growth factors revealed both synergistic and antagonistic effects on protein synthesis and expression levels with PDGF showing dominance over both IGF-1 and EGF in generating distinct proteome compositions. Using signaling pathway inhibitors, PI3K was identified as an early site for signal diversification, with sustained activity of the PI3K/AKT pathway critical for regulating late protein synthesis and phosphorylation of target proteins and required for maintaining the PDGF-dependent motile phenotype. Several proteins were identified with novel PI3K/Akt-dependent synthesis and phosphorylations including eEF2, PRS7, RACK-1, acidic calponin, NAP1L1, Hsp73, and fascin. The data also reveal induction/suppression of key F-actin and actomyosin regulators and chaperonins that enable PDGFR to direct the assembly of a motile cytoskeleton, despite simultaneous antagonistic signaling activities. Together, the study demonstrates that long-term exposure to different growth factors results in receptor tyrosine kinase-specific regulation of relatively small subproteomes, and implies that the strength and longevity of receptor tyrosine kinase-specific signals are critical in defining the composition and functional activity of the resulting proteome.
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Affiliation(s)
- Kohji Nagano
- Discovery Research Department, Chugai Pharmaceutical Co. Ltd., Japan
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Salivary Protein Profiles among HER2/neu-Receptor-Positive and -Negative Breast Cancer Patients: Support for Using Salivary Protein Profiles for Modeling Breast Cancer Progression. JOURNAL OF ONCOLOGY 2012; 2012:413256. [PMID: 22570650 PMCID: PMC3335259 DOI: 10.1155/2012/413256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 01/17/2012] [Indexed: 12/29/2022]
Abstract
Purpose. The objective of this study was to compare the salivary protein profiles from individuals diagnosed with breast cancer that were either HER2/neu receptor positive or negative. Methods. Two pooled saliva specimens underwent proteomic analysis. One pooled specimen was from women diagnosed with stage IIa HER2/neu-receptor-positive breast cancer patients (n = 10) and the other was from women diagnosed with stage IIa HER2/neu-receptor-negative cancer patients (n = 10). The pooled samples were trypsinized and the peptides labeled with iTRAQ reagent. Specimens were analyzed using an LC-MS/MS mass spectrometer. Results. The results yielded approximately 71 differentially expressed proteins in the saliva specimens. There were 34 upregulated proteins and 37 downregulated proteins.
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Teo SM, Pawitan Y, Kumar V, Thalamuthu A, Seielstad M, Chia KS, Salim A. Multi-platform segmentation for joint detection of copy number variants. Bioinformatics 2011; 27:1555-61. [PMID: 21471018 DOI: 10.1093/bioinformatics/btr162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION With the expansion of whole-genome studies, there is rapid evolution of genotyping platforms. This leads to practical issues such as upgrading of genotyping equipment which often results in research groups having data from different platforms for the same samples. While having more data can potentially yield more accurate copy-number estimates, combining such data is not straightforward as different platforms show different degrees of attenuation of the true copy-number or different noise characteristics and marker panels. Currently, there is still a relative lack of procedures for combining information from different platforms. RESULTS We develop a method, called MPSS, based on a correlated random-effect model for the unobserved patterns and extend the robust smooth segmentation approach to the multiple-platform scenario. We also propose an objective criterion for discrete segmentation required for downstream analyses. For each identified segment, the software reports a P-value to indicate the likelihood of the segment being a true CNV. From the analyses of real and simulated data, we show that MPSS has better operating characteristics when compared to single-platform methods, and have substantially higher sensitivity compared to an existing multiplatform method. AVAILABILITY The methods are implemented in an R package MPSS, and the source is available from http://www.meb.ki.se/~yudpaw.
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Affiliation(s)
- Shu Mei Teo
- Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore
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Damaraju S, Zhang N, Li N, Tao L, Damaraju VL, Dufour J, Santos C, Sun XJ, Mackey J, Wishart DS, Cass CE, Li L. Evidence for copurification of micronuclei in sucrose density gradient-enriched plasma membranes from cell lines. Anal Biochem 2009; 396:69-75. [PMID: 19699175 DOI: 10.1016/j.ab.2009.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 08/06/2009] [Accepted: 08/17/2009] [Indexed: 11/26/2022]
Abstract
Sucrose density gradient-enriched membrane preparations and membrane fraction enrichment through affinity purification techniques are commonly used in proteomic analysis. However, published proteomic profiles characterized by the above methods show the presence of nuclear proteins in addition to membrane proteins. While shuttling of nuclear proteins across cellular compartments and their transient residency at membrane interfaces could explain some of these observations, the presence of nuclear proteins in proteomic profiles generated with crude and enriched membranes could be the result of nonspecific contamination of nuclear debris during cell fractionation procedures. We hypothesized that micronuclei arising from the genomic instability inherent to cancer cells may copurify with plasma membrane fractions on sucrose gradients. Using sucrose gradient-enriched plasma membranes from breast cancer cell lines derived from the MCF-7 cell line, we provide experimental evidence to indicate that micronuclei are present in fresh preparations of plasma membranes. The origin of these micronuclei was traced to budding of nuclei in intact cells. Furthermore, mass spectrometric analysis confirmed the presence of nuclear proteins as well as membrane and associated signaling proteins in sucrose gradient-enriched preparations.
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Affiliation(s)
- Sambasivarao Damaraju
- PolyomX Program, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada T6G 1Z2
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Hajduch M, Skalnikova H, Halada P, Vydra D, Dzubak P, Dziechciarkova M, Strnad M, Radioch D, Gadher SJ, Kovarova H. Cyclin-Dependent Kinase Inhibitors and Cancer: Usefulness of Proteomic Approaches in Assessment of the Molecular Mechanisms and Efficacy of Novel Therapeutics. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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Desrivières S, Kuhn K, Müller J, Gläser M, Laria NCP, Korder J, Sonnentag M, Neumann T, Schwarz J, Schäfer J, Hamon C, Groner B, Prinz T. Comparison of the nuclear proteomes of mammary epithelial cells at different stages of functional differentiation. Proteomics 2007; 7:2019-37. [PMID: 17514683 DOI: 10.1002/pmic.200600994] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The progression of stem cells to proliferating progenitor cells and finally to a quiescent differentiated state is a hallmark of organ development. This process proceeds through distinct steps and is regulated through cell-cell interactions and by systemically and locally acting factors. We have established a cell culture system which recapitulates features of mammary gland development in vitro and allows the comparison of three characteristic differentiation stages. Cell fate decisions relating to proliferation and differentiation are dependent on the function of proteins in the nucleus. Therefore, we have applied proteomic approaches, including 1- and 2-DE coupled with MS and a gel-free system, called protein sequence tag technology (PST), to assess the changes in the nuclear protein composition during differentiation of mammary epithelial cells. We identified about 250 individual proteins which are present in the nucleus of proliferating and functionally differentiated mammary epithelial cells. We functionally categorised the differentially expressed proteins and identified a multitude of proteins that regulate gene expression at the transcriptional or post-transcriptional level. This analysis greatly enriches our global view of the dynamic changes of nuclear proteins during the development of mammary epithelial cells and suggests models for the control of differentiation-specific protein expression.
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Maloney A, Clarke PA, Naaby-Hansen S, Stein R, Koopman JO, Akpan A, Yang A, Zvelebil M, Cramer R, Stimson L, Aherne W, Banerji U, Judson I, Sharp S, Powers M, deBilly E, Salmons J, Walton M, Burlingame A, Waterfield M, Workman P. Gene and Protein Expression Profiling of Human Ovarian Cancer Cells Treated with the Heat Shock Protein 90 Inhibitor 17-Allylamino-17-Demethoxygeldanamycin. Cancer Res 2007; 67:3239-53. [PMID: 17409432 DOI: 10.1158/0008-5472.can-06-2968] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The promising antitumor activity of 17-allylamino-17-demethoxygeldanamycin (17AAG) results from inhibition of the molecular chaperone heat shock protein 90 (HSP90) and subsequent degradation of multiple oncogenic client proteins. Gene expression microarray and proteomic analysis were used to profile molecular changes in the A2780 human ovarian cancer cell line treated with 17AAG. Comparison of results with an inactive analogue and an alternative HSP90 inhibitor radicicol indicated that increased expression of HSP72, HSC70, HSP27, HSP47, and HSP90beta at the mRNA level were on-target effects of 17AAG. HSP27 protein levels were increased in tumor biopsies following treatment of patients with 17AAG. A group of MYC-regulated mRNAs was decreased by 17AAG. Of particular interest and novelty were changes in expression of chromatin-associated proteins. Expression of the heterochromatin protein 1 was increased, and expression of the histone acetyltransferase 1 and the histone arginine methyltransferase PRMT5 was decreased by 17AAG. PRMT5 was shown to be a novel HSP90-binding partner and potential client protein. Cellular protein acetylation was reduced by 17AAG, which was shown to have an antagonistic interaction on cell proliferation with the histone deacetylase inhibitor trichostatin A. This mRNA and protein expression analysis has provided new insights into the complex molecular pharmacology of 17AAG and suggested new genes and proteins that may be involved in response to the drug or be potential biomarkers of drug action.
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Affiliation(s)
- Alison Maloney
- Haddow Laboratories, Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Surrey, United Kingdom
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Deng SS, Xing TY, Zhou HY, Xiong RH, Lu YG, Wen B, Liu SQ, Yang HJ. Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human. GENOMICS PROTEOMICS & BIOINFORMATICS 2007; 4:165-72. [PMID: 17127214 PMCID: PMC5054074 DOI: 10.1016/s1672-0229(06)60029-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF-MS), incorporated with online database searching, were performed to investigate differential proteins of breast cancer and adjacent normal breast tissues. Considering that serum albumin is abundantly presented in normal control samples, 15 differential spots detected in 11 out of 12 (91.7%) breast cancer samples were identified by online SIENA-2DPAGE database searching and MALDI-TOF/TOF-MS analysis. The results indicate that pathological changes of breast cancer are concerned with augmentation of substance metabolism, promotion of proteolytic activity, decline of activity of some inhibitors of enzymes, and so on. Some important proteins involved in the pathological process of breast cancer with changed expression may be useful biomarkers, such as alpha-1-antitrypsin, EF-1-beta, cathepsin D, TCTP, SMT3A, RPS12, and PSMA1, among which SMT3A, RPS12, and PSMA1 were first reported for breast cancer in this study.
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Affiliation(s)
- Shi-Shan Deng
- Department of Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu610041, China
| | - Tian-Yong Xing
- Affiliated Hospital of North Sichuan Medical College, Nanchong637000, China
| | - Hong-Ying Zhou
- Department of Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu610041, China
| | - Ruo-Hong Xiong
- Department of Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu610041, China
| | - You-Guang Lu
- Department of Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu610041, China
| | - Bin Wen
- Department of Pathology, Preclinical Medicine School, North Sichuan Medical College, Nanchong637000, China
| | - Shang-Qing Liu
- Department of Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu610041, China
| | - Hui-Jun Yang
- Department of Anatomy, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu610041, China
- Corresponding author.
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Meunier B, Dumas E, Piec I, Béchet D, Hébraud M, Hocquette JF. Assessment of Hierarchical Clustering Methodologies for Proteomic Data Mining. J Proteome Res 2006; 6:358-66. [PMID: 17203979 DOI: 10.1021/pr060343h] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hierarchical clustering methodology is a powerful data mining approach for a first exploration of proteomic data. It enables samples or proteins to be grouped blindly according to their expression profiles. Nevertheless, the clustering results depend on parameters such as data preprocessing, between-profile similarity measurement, and the dendrogram construction procedure. We assessed several clustering strategies by calculating the F-measure, a widely used quality metric. The combination, on logged matrix, of Pearson correlation and Ward's methods for data aggregation is among the best clustering strategies, at least with the data sets we studied. This study was carried out using PermutMatrix, a freely available software derived from transcriptomics.
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Affiliation(s)
- Bruno Meunier
- UR 1213, Unité de Recherches sur les Herbivores, Equipe Croissance et Métabolisme du Muscle, INRA de Clermont-Ferrand/Theix, F-63122 [corrected] Saint-Genès Champanelle, France.
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Ghafouri B, Irander K, Lindbom J, Tagesson C, Lindahl M. Comparative proteomics of nasal fluid in seasonal allergic rhinitis. J Proteome Res 2006; 5:330-8. [PMID: 16457599 DOI: 10.1021/pr050341h] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A comparative proteomic approach was applied to examine nasal lavage fluid (NLF) from patients with seasonal allergic rhinitis (SAR, n = 6) and healthy subjects (controls, n = 5). NLF samples were taken both before allergy (pollen) season and during season, and proteins were analyzed by two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) after tryptic cleavage. Twenty proteins were selected and quantified. During allergy season, the levels of six sialylated isoforms of PLUNC (palate lung nasal epithelial clone) were lower in SAR patients than controls, as were the levels of six isoforms of von Ebner's gland protein (VEGP), including a previously undescribed form with N-linked glycosylation, and of cystatin S. PLUNC is a new innate immunity protein and VEGP and cystatin S are two endogenous proteinase inhibitors. By contrast, the levels of an acidic form of alpha-1-antitrypsin were higher in SAR patients than controls. One previously unidentified NLF protein was found in all samples from the SAR patients during allergy season but not in any sample before allergy season: this protein was identified as eosinophil lysophospholipase (Charcot-Leyden crystal protein/galactin 10). MS/MS analysis of the N-terminus of the protein showed removal of Met and acetylation of Ser. Altogether, these findings illustrate the potential use of proteomics for identifying protein changes associated with allergic rhinitis and for revealing post-translational modifications of such new potential markers of allergic inflammation.
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Affiliation(s)
- B Ghafouri
- Division of Occupational and Environmental Medicine, Department of Molecular and Clinical Medicine, Linköping University, Sweden
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Pardo M, García A, Thomas B, Piñeiro A, Akoulitchev A, Dwek RA, Zitzmann N. Proteome analysis of a human uveal melanoma primary cell culture by 2-DE and MS. Proteomics 2005; 5:4980-93. [PMID: 16267820 DOI: 10.1002/pmic.200500030] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We present here the first proteomics analysis of uveal melanoma (UM) cells. These cells represent a good model for the identification of polypeptide markers, which could be developed as diagnostic tools. UM is the most common primary intraocular tumour in adults. In contrast to other cancers, the survival rate of patients with this malignancy has changed little over the past few decades; a better understanding of the molecular biology of UM oncogenesis and metastasis is needed to build the basis for the identification of novel drug targets. In the study presented here, proteins from a UM primary cell culture were separated by 2-DE using a pI 3-10 gradient; 270 spots were analysed by LC-MS/MS, identifying 683 proteins derived from 393 different genes. Of those, 69 (18%) are related to cancer processes involving cell division, proliferation, invasion, metastasis, oncogenesis, drug resistance and others. To our knowledge, 96% of the proteins identified, including 16 hypothetical proteins, have never been reported in UM before. This study represents the first step towards the establishment of a UM protein database as a valuable resource for the study of this malignancy.
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Affiliation(s)
- María Pardo
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Korsching E, Packeisen J, Liedtke C, Hungermann D, Wülfing P, van Diest PJ, Brandt B, Boecker W, Buerger H. The origin of vimentin expression in invasive breast cancer: epithelial-mesenchymal transition, myoepithelial histogenesis or histogenesis from progenitor cells with bilinear differentiation potential? J Pathol 2005; 206:451-7. [PMID: 15906273 DOI: 10.1002/path.1797] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Vimentin expression is a rather rare finding in invasive breast cancer, and is associated with high tumour invasiveness and chemoresistance. It is currently explained by two different biological theories: direct histogenetic derivation from myoepithelial cells, and epithelial-mesenchymal transition (EMT) reflecting the end-stage of breast cancer dedifferentiation. In this study we aimed to obtain further insights into the biological hallmarks of these vimentin-expressing breast cancers. We applied immunohistochemistry for vimentin and 15 other differentiation markers to a series of 364 invasive breast cancer cases, using tissue microarray technology. 7.7% of all tumours expressed vimentin. Almost all of these cases (19/21) were Grade 3 invasive ductal carcinomas, and the majority (13/21) of these were associated with a ductal in situ component. Vimentin expression was also seen in the respective in situ components and correlated positively with the expression of SMA, CD10, CK 5, p53, Mib-1 and EGFR. A negative correlation was seen for the expression of CK 8/18 and the oestrogen receptor. Vimentin-expressing carcinomas revealed a significantly higher average absolute number of cytogenetic alterations per case, but a significantly lower frequency of chromosome 16q losses compared to vimentin-negative cases. Our present results demonstrate that, despite analogies between vimentin-positive breast cancers and myoepithelial cells in their expression of differentiation-related proteins, neither myoepithelial histogenesis nor EMT can exclusively explain the biology of these distinct tumours. This is mainly supported by the significantly higher incidence of vimentin-expressing breast cancers compared to any other myoepithelial breast tumours and the fact that vimentin is already observed in ductal in situ components. We therefore propose the alternative hypothesis that vimentin-expressing breast carcinomas may derive from breast progenitor cells with bilinear (glandular and myoepithelial) differentiation potential.
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15
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Wu X, Xiao Z, Chen Z, Li C, Li J, Feng X, Yi H, Liang S, Chen P. Differential analysis of two-dimension gel electrophoresis profiles from the normal-metaplasia-dysplasia-carcinoma tissue of human bronchial epithelium. Pathol Int 2005; 54:765-73. [PMID: 15482566 DOI: 10.1111/j.1440-1827.2004.01753.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Processes involved in malignant transformation of the lung from preneoplasia are poorly understood. To better understand this process, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) profiles of proteins from the normal, metaplasia, dysplasia and carcinoma tissues of human bronchial epithelia were examined by differential proteomic analysis. The selected differential protein-spots were identified by peptide mass fingerprint based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and database searching. The average spots for normal epithelium, metaplasia, dysplasia and invasive carcinoma were 1189.50 +/- 39.89, 1227.00 +/- 37.90, 1273.00 +/- 43.31 and 1326.00 +/- 66.63, respectively. Well-resolved, reproducible 2-D PAGE patterns of the normal-metaplasia-dysplasia-carcinoma tissues of bronchial epithelia were obtained. After matching, the number of spots of differential proteins between normal tissue and metaplasia, metaplasia and dysplasia, and dysplasia and invasive cancer tissues were 31.50 +/- 7.67, 41.00 +/- 9.07 and 56.00 +/- 8.96, respectively. In total, 35 differential proteins, expressed only at the later stage of a two-stage comparison, were identified, some of which are known to be involved in regulating the processes of proliferation, differentiation and signal transduction. Current data in this study, for the first time, provide the basis for identification of potential tumor markers of human lung squamous carcinoma and their involvement in the progression of malignant transformation of bronchial epithelium.
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Affiliation(s)
- Xiaoying Wu
- Medical Research Center, Xiangya Hospital, Changsha, China
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16
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Meleth S, Deshane J, Kim H. The case for well-conducted experiments to validate statistical protocols for 2D gels: different pre-processing = different lists of significant proteins. BMC Biotechnol 2005; 5:7. [PMID: 15707480 PMCID: PMC553976 DOI: 10.1186/1472-6750-5-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Accepted: 02/11/2005] [Indexed: 11/15/2022] Open
Abstract
Background The proteomics literature has seen a proliferation of publications that seek to apply the rapidly improving technology of 2D gels to study various biological systems. However, there is a dearth of systematic studies that have investigated appropriate statistical approaches to analyse the data from these experiments. Results Comparison of the effects of statistical pre-processing on the results of two sample t-tests suggests that the results of 2D gel experiments and by extension the conclusions derived from these experiments are not independent of the statistical protocol used. Conclusions This study suggests that there is a need for well-conducted validation studies to establish optimal statistical techniques to be used on such data sets.
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Affiliation(s)
- Sreelatha Meleth
- Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jessy Deshane
- Department of Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35924 USA
| | - Helen Kim
- Department of Pharmacology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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17
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Korsching E, Packeisen J, Helms MW, Kersting C, Voss R, van Diest PJ, Brandt B, van der Wall E, Boecker W, Bürger H. Deciphering a subgroup of breast carcinomas with putative progression of grade during carcinogenesis revealed by comparative genomic hybridisation (CGH) and immunohistochemistry. Br J Cancer 2004; 90:1422-8. [PMID: 15054466 PMCID: PMC2409666 DOI: 10.1038/sj.bjc.6601658] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Distinct parallel cytogenetic pathways in breast carcinogenesis could be identified in recent years. Nevertheless, it remained unclear as to which tumours may have progressed in grade or which patterns of cytogenetic alteration may define the switch from an in situ towards an invasive lesion. In order to gain more detailed insights into cytogenetic mechanisms of the pathogenesis of breast cancer, the chromosomal imbalances of 206 invasive breast cancer cases were characterised by means of comparative genomic hybridisation (CGH). CGH data were subjected to hierarchical cluster analysis and the results were further compared with immunohistochemical findings on tissue arrays from the same breast cancer cases. The combined analysis of immunohistochemical and cytogenetic data provided evidence that carcinomas with gains of 7p, and to a lesser extent losses of 9q and gains of 5p, are a distinct subgroup within the spectrum of ductal invasive grade 3 breast carcinomas. These aberrations were associated with a high degree of cytogenetic instability (16.6 alterations per case on average), 16q-losses in over 70% of these cases, strong oestrogen receptor expression and absence of strong expression of p53, c-erbB2 and Ck 5. These characteristics provide strong support for the hypothesis that these tumours may develop through stages of well- and perhaps intermediately differentiated breast cancers. Our results therefore underline the existence of several parallel and also stepwise progression pathways towards breast cancer.
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Affiliation(s)
- E Korsching
- Institute of Pathology, University of Münster, Domagkstr. 17, 48149 Münster, Germany
| | - J Packeisen
- Institute of Pathology, Klinikum Osnabrück, Domagkstr. 17, 48149 Münster, Germany
| | - M W Helms
- Laboratory Medicine, Institute of Clinical Chemistry, University of Münster, Domagkstr. 17, 48149 Münster, Germany
| | - C Kersting
- Institute of Pathology, University of Münster, Domagkstr. 17, 48149 Münster, Germany
| | - R Voss
- Institute of Atherosclerosis Research, University of Münster, Domagkstr. 17, 48149 Münster, Germany
| | - P J van Diest
- Institute of Pathology, Utrecht University Medical Center, The Netherlands
| | - B Brandt
- Laboratory Medicine, Institute of Clinical Chemistry, University of Münster, Domagkstr. 17, 48149 Münster, Germany
| | - E van der Wall
- Department of Medical Oncology, Utrecht University Medical Center, The Netherlands
| | - W Boecker
- Institute of Pathology, University of Münster, Domagkstr. 17, 48149 Münster, Germany
| | - H Bürger
- Institute of Pathology, University of Münster, Domagkstr. 17, 48149 Münster, Germany
- Institute of Pathology, University of Münster, Domagkstr. 17, 48149 Münster, Germany. E-mail:
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18
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Soares HD, Williams SA, Snyder PJ, Gao F, Stiger T, Rohlff C, Herath A, Sunderland T, Putnam K, White WF. Proteomic Approaches in Drug Discovery and Development. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2004; 61:97-126. [PMID: 15482813 DOI: 10.1016/s0074-7742(04)61005-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Affiliation(s)
- Holly D Soares
- Pfizer Global Research and Development, Groton, CT 06340, USA
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19
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Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. MASS SPECTROMETRY REVIEWS 2004; 23:34-44. [PMID: 14625891 DOI: 10.1002/mas.10066] [Citation(s) in RCA: 310] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The overall history and recent advancements in Surface-Enhanced Laser Desorption/Ionization (SELDI) affinity technology is reviewed. A detailed account of SELDI technology, utilizing Immobilized-Metal Affinity surfaces, pseudo-specific chromatographic surfaces, and biospecific interactive surfaces, is presented with particular emphasis placed upon examination of fundamental characteristics as well as specific applications for each. Finally, a detailed review of the specific use of such affinity surfaces in fundamental aspects of clinical, process, and research proteomics activity is presented.
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Affiliation(s)
- Ning Tang
- Ciphergen Biosystems, 6611 Dumbarton Circle, Fremont, California 94555, USA
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20
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Dwek MV, Alaiya AA. Proteome analysis enables separate clustering of normal breast, benign breast and breast cancer tissues. Br J Cancer 2003; 89:305-7. [PMID: 12865921 PMCID: PMC2394238 DOI: 10.1038/sj.bjc.6601008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We have used proteomics with cluster analysis for the classification of breast tumour tissues. In our approach, we can distinguish between normal breast, benign breast and breast cancer tissues on the basis of the protein expression profiles. We propose an objective method for the classification of breast tumour specimens.
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Affiliation(s)
- M V Dwek
- School of Biosciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK.
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21
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Baak JPA, Path FRC, Hermsen MAJA, Meijer G, Schmidt J, Janssen EAM. Genomics and proteomics in cancer. Eur J Cancer 2003; 39:1199-215. [PMID: 12763207 DOI: 10.1016/s0959-8049(03)00265-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cancer development is driven by the accumulation of DNA changes in the approximately 40000 chromosomal genes. In solid tumours, chromosomal numerical/structural aberrations are common. DNA repair defects may lead to genome-wide genetic instability, which can drive further cancer progression. The genes code the actual players in the cellular processes, the 100000-10 million proteins, which in (pre)malignant cells can also be altered in a variety of ways. Over the past decade, our knowledge of the human genome and Genomics (the study of the human genome) in (pre)malignancies has increased enormously and Proteomics (the analysis of the protein complement of the genome) has taken off as well. Both will play an increasingly important role. In this article, a short description of the essential molecular biological cell processes is given. Important genomic and proteomic research methods are described and illustrated. Applications are still limited, but the evidence so far is exciting. Will genomics replace classical diagnostic or prognostic procedures? In breast cancers, the gene expression array is stronger than classical criteria, but in endometrial hyperplasia, quantitative morphological features are more cost-effective than genetic testing. It is still too early to make strong statements, the more so because it is expected that genomics and proteomics will expand rapidly. However, it is likely that they will take a central place in the understanding, diagnosis, monitoring and treatment of (pre)cancers of many different sites.
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Affiliation(s)
- J P A Baak
- Department of Pathology, Central Hospital for Rogaland, Box 8001, 4068 Stavanger, Norway.
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22
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Abstract
Proteome technology has been used widely in cancer research and is a useful tool for the identification of new cancer markers and treatment-related changes in cancer. This article details the use of proteome technology in cancer research, and laboratory-based and clinical cancer research studies are described. New developments in proteome technology that enable higher sample-throughput are evaluated and methods for enhancing conventional proteome analysis (based on two-dimensional electrophoresis) discussed. The need to couple laboratory-based proteomics research with clinically relevant models of the disease is also considered, as this remains the next main challenge of cancer-related proteome research.
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Affiliation(s)
- Miriam V Dwek
- Breast Cancer Research Group, Department of Surgery, Royal Free and University College London Medical School, Institute of Surgical Studies, UK.
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23
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Panaretou B, Siligardi G, Meyer P, Maloney A, Sullivan JK, Singh S, Millson SH, Clarke PA, Naaby-Hansen S, Stein R, Cramer R, Mollapour M, Workman P, Piper PW, Pearl LH, Prodromou C. Activation of the ATPase activity of hsp90 by the stress-regulated cochaperone aha1. Mol Cell 2002; 10:1307-18. [PMID: 12504007 DOI: 10.1016/s1097-2765(02)00785-2] [Citation(s) in RCA: 393] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Client protein activation by Hsp90 involves a plethora of cochaperones whose roles are poorly defined. A ubiquitous family of stress-regulated proteins have been identified (Aha1, activator of Hsp90 ATPase) that bind directly to Hsp90 and are required for the in vivo Hsp90-dependent activation of clients such as v-Src, implicating them as cochaperones of the Hsp90 system. In vitro, Aha1 and its shorter homolog, Hch1, stimulate the inherent ATPase activity of yeast and human Hsp90. The identification of these Hsp90 cochaperone activators adds to the complex roles of cochaperones in regulating the ATPase-coupled conformational changes of the Hsp90 chaperone cycle.
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Affiliation(s)
- Barry Panaretou
- Division of Life Sciences, Franklin-Wilkins Building, 150 Stamford Street, SE1 9NN, London, United Kingdom
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24
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Korsching E, Packeisen J, Agelopoulos K, Eisenacher M, Voss R, Isola J, van Diest PJ, Brandt B, Boecker W, Buerger H. Cytogenetic alterations and cytokeratin expression patterns in breast cancer: integrating a new model of breast differentiation into cytogenetic pathways of breast carcinogenesis. J Transl Med 2002; 82:1525-33. [PMID: 12429812 DOI: 10.1097/01.lab.0000038508.86221.b3] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The introduction of a concept proposing multiple cellular subgroups in the normal female breast, including cytokeratin 5/6 (Ck 5/6)-positive progenitor cells, offers a new explanation for the existence of highly aggressive breast cancers with and without Ck 5/6 expression. Using the tissue microarray technique, 166 breast cancer cases, all characterized by comparative genomic hybridization, were evaluated by immunohistochemistry, using 15 different antibodies (estrogen receptor, progesterone receptor, p53, Ki-67, c-erbB2, epidermal growth factor receptor, cyclins A, D1, and E, bcl-2, p21, p27, Ck 5/6, Ck 8/18, and smooth muscle actin) and chromogenic in situ hybridization for c-erbB2. Biomathematical cluster analysis was applied to confirm the conventional interpretation of the results by an independent approach. Ck 5/6-positive breast carcinomas were in general negative for estrogen receptor and progesterone receptor, were highly proliferating (as reflected by Ki67 and cyclin A), and were associated with specific protein expression patterns, such as expression of p53 and epithelial growth factor receptor (all related to more aggressive tumor behavior), which could further be demonstrated by biomathematical cluster analysis. In contrast Ck 5/6-negative breast carcinomas revealed a lower tumor proliferation rate, an increased expression of p21, p27, c-erbB2, and bcl-2, and a significantly lower number of genetic alterations, with losses of chromosomal material of 16q as the most common genetic alteration. Our data give the first hints to the hypothesis that different cellular subgroups in the female breast give rise to subgroups of breast carcinomas with differing protein expression and cytogenetic alteration patterns that may be related to clinical behavior.
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25
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Stein RC, Zvelebil MJ. The application of 2D gel-based proteomics methods to the study of breast cancer. J Mammary Gland Biol Neoplasia 2002; 7:385-93. [PMID: 12882523 DOI: 10.1023/a:1024034031472] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The protein complement of breast cells consists of many thousands of proteins. Recent developments in 2D gel electrophoresis technology have made studies requiring the quantitative analysis of a differential proteome, such as comparison between normal and malignant cells or investigation of drug effects on cells, truly feasible. Computer software plays a central part in the comparisons between multiple gels required for such experiments. In addition, software tools allow patterns of coexpression of proteins to be studied, offering potential insights into protein regulation, interactions, and functions, especially when combined with complementary data on gene expression. In this paper, the technology and limitations of 2D gel-based proteomics are reviewed. Techniques for comparing sets of gels at a global level as well as identifying specific protein features that differentiate gels are discussed. Our own experience of studying the breast cell proteome is used to illustrate the difficulties and achievements of differential proteomics.
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Affiliation(s)
- Robert C Stein
- Ludwig Institute for Cancer Research & Department of Oncology, University College London, London, United Kingdom
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26
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Abstract
The study of the development of the mammary gland at the molecular level in animals is difficult because of the complex tissue organization. This review introduces a proteomic approach to investigate mammary gland development in a cell culture system that we have previously developed as an in vitro model for studying mammary cell differentiation. The model is based on two cell lines, one of which is able to differentiate spontaneously and produce hemispherical blisters, called domes, when confluent. Through proteomic dissection of dome-forming cells, two types of key regulatory genes have been identified: genes inducing cellular structural modifications and genes related to functional modifications. We identified several genes in the pathway leading to dome formation in vitro and showed that the functional and structural changes taking place in dome-forming cells correspond to cellular changes occurring in vivo when tubules and alveoli are developed in the mammary gland at pregnancy.
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Affiliation(s)
- I Zucchi
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.
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27
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Kovarova H, Halada P, Man P, Dzubak P, Hajduch M. Application of proteomics in the search for novel proteins associated with the anti-cancer effect of the synthetic cyclin-dependent kinases inhibitor, bohemine. Technol Cancer Res Treat 2002; 1:247-56. [PMID: 12625783 DOI: 10.1177/153303460200100405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The purpose of this study was to use the proteomics approach, which is based on high resolution two-dimensional electrophoresis coupled with multivariate correspondence analysis and mass spectrometry, to classify objectively the biochemical basis of the anti-cancer activity of the synthetic cyclin-dependent kinase inhibitor, bohemine (BOH). The changes in the cell cycle and corresponding protein composition of the A549 human lung adenocarcinoma cell line after treatment with BOH were evaluated and proteins differentially expressed in the BOH treated A549 cells, compared to the untreated A549 counterparts, were selected. Thirteen of these candidate proteins associated with the drug effects in vitro were identified by mass spectrometry. Many of these proteins fall into one of three functional categories: i) metabolic pathways (glycolysis, nucleic acid synthesis and NADPH production), ii) stress response and protein folding, and iii) cytoskeleton and exocytosis. Changes in protein expression patterns corresponded to a higher resistance of A549 lung carcinoma cells to BOH when compared to the CEM leukaemia cell line. These protein changes reflect a fine balance of the resistant versus the susceptible phenotype in response to the drug. Since BOH is a selective cyclin-dependent kinase inhibitor, changes in the protein expression pattern can be more generally associated with cell cycle regulation as evidenced by inhibition of cell cycling in A549 cells. Our conclusions further underline the importance of cell cycle control in both the cellular signalling and metabolic pathways.
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Affiliation(s)
- Hana Kovarova
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic
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28
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Benvenuti S, Cramer R, Bruce J, Waterfield MD, Jat PS. Identification of novel candidates for replicative senescence by functional proteomics. Oncogene 2002; 21:4403-13. [PMID: 12080471 DOI: 10.1038/sj.onc.1205525] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2002] [Revised: 03/26/2002] [Accepted: 03/26/2002] [Indexed: 11/08/2022]
Abstract
To identify the underlying mechanisms that limit the mitotic potential of normal somatic cells, we have undertaken a high resolution differential proteomic analysis aimed at identifying proteins that were differentially expressed upon replicative senescence. Since replicative senescence in heterogeneous primary fibroblast cultures is asynchronous, we analysed a group of conditionally immortalized rat embryo fibroblast cell lines that have previously been shown to undergo synchronous senescence upon inactivation of SV40 tsA58 T antigen. This identified 43 spots that were differentially expressed in these cell lines. Comparison of the identity of these features with those identified in a complimentary independent differential proteomic analysis of replicative senescence, directly in primary rat embryo fibroblasts upon serial passaging, identified nine features that were in common between the two studies even though they had been conducted entirely separately. None of these proteins have previously been recognized to be involved with replicative senescence. Thus, they represent novel starting points for elucidating the underlying mechanism that regulates the finite mitotic life span of somatic cells and how it can be overcome in cancer cells.
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Affiliation(s)
- Silvia Benvenuti
- Ludwig Institute for Cancer Research, Royal Free and University College School of Medicine, Courtauld Building, 91 Riding House Street, London W1W 7BS, UK
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29
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Sauter ER, Zhu W, Fan XJ, Wassell RP, Chervoneva I, Du Bois GC. Proteomic analysis of nipple aspirate fluid to detect biologic markers of breast cancer. Br J Cancer 2002; 86:1440-3. [PMID: 11986778 PMCID: PMC2375367 DOI: 10.1038/sj.bjc.6600285] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2001] [Revised: 02/21/2002] [Accepted: 02/27/2002] [Indexed: 11/10/2022] Open
Abstract
The early detection of breast cancer is the best means to minimise disease-related mortality. Current screening techniques have limited sensitivity and specificity. Breast nipple aspirate fluid can be obtained noninvasively and contains proteins secreted from ductal and lobular epithelia. Nipple aspirate fluid proteins are breast specific and generally more concentrated than corresponding blood levels. Proteomic analysis of 1 microl of diluted nipple aspirate fluid over a 5-40 kDa range from 20 subjects with breast cancer and 13 with nondiseased breasts identified five differentially expressed proteins. The most sensitive and specific proteins were 6500 and 15 940 Da, found in 75-84% of samples from women with cancer but in only 0-9% of samples from normal women. These findings suggest that (1) differential expression of nipple aspirate fluid proteins exists between women with normal and diseased breasts, and (2) analysis of these proteins may predict the presence of breast cancer.
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Affiliation(s)
- Edward R Sauter
- Department of Surgery, Thomas Jefferson University, 1025 Walnut St., Ste 605, Philadelphia, PA 19107, USA.
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30
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Benvenuti S, Cramer R, Quinn CC, Bruce J, Zvelebil M, Corless S, Bond J, Yang A, Hockfield S, Burlingame AL, Waterfield MD, Jat PS. Differential proteome analysis of replicative senescence in rat embryo fibroblasts. Mol Cell Proteomics 2002; 1:280-92. [PMID: 12096110 DOI: 10.1074/mcp.m100028-mcp200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Normal somatic cells undergo a finite number of divisions and then cease dividing whereas cancer cells are able to proliferate indefinitely. To identify the underlying mechanisms that limit the mitotic potential, a two-dimensional differential proteome analysis of replicative senescence in serially passaged rat embryo fibroblasts was undertaken. Triplicate independent two-dimensional gels containing over 1200 spots each were run, curated, and analyzed. This revealed 49 spots whose expression was altered more than 2-fold. Of these, 42 spots yielded positive protein identification by mass spectrometry comprising a variety of cytoskeletal, heat shock, and metabolic proteins, as well as proteins involved in trafficking, differentiation, and protein synthesis, turnover, and modification. These included gelsolin, a candidate tumor suppressor for breast cancer, and alpha-glucosidase II, a member of the family of glucosidases that includes klotho; a defect in klotho expression in mice results in a syndrome that resembles human aging. Changes in expression of TUC-1, -2, -4, and -4 beta, members of the TUC family critical for neuronal differentiation, were also identified. Some of the identified changes were also shown to occur in two other models of senescence, premature senescence of REF52 cells and replicative senescence of mouse embryo fibroblasts. The majority of these candidate proteins were unrecognized previously in replicative senescence. They are now implicated in a new role.
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MESH Headings
- Animals
- Blotting, Western
- Cell Line
- Cells, Cultured
- Cellular Senescence
- Chromatography, High Pressure Liquid
- Cytoskeleton/metabolism
- Electrophoresis, Gel, Two-Dimensional
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Gelsolin/biosynthesis
- Glucuronidase
- Klotho Proteins
- Membrane Proteins/biosynthesis
- Rats
- Rats, Sprague-Dawley
- Reverse Transcriptase Polymerase Chain Reaction
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Up-Regulation
- alpha-Glucosidases/biosynthesis
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Affiliation(s)
- Silvia Benvenuti
- Ludwig Institute for Cancer Research, Royal Free and University College School of Medicine, Courtauld Building, 91 Riding House Street, London W1W 7BS, United Kingdom
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31
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2448432 DOI: 10.1002/cfg.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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