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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kaczmarek MM, Myszczyński K, Kiśluk J, Majewska A, Michalska-Falkowska A, Kodzik N, Reszeć J, Sierko E, Nikliński J. Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype. PLoS One 2022; 17:e0268073. [PMID: 35512017 PMCID: PMC9071164 DOI: 10.1371/journal.pone.0268073] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Monika M. Kaczmarek
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Majewska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Natalia Kodzik
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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Vezenkov LL, Sanchez CA, Bellet V, Martin V, Maynadier M, Bettache N, Lisowski V, Martinez J, Garcia M, Amblard M, Hernandez JF. Structure-Activity Relationships of JMV4463, a Vectorized Cathepsin D Inhibitor with Antiproliferative Properties: The Unique Role of the AMPA-Based Vector. ChemMedChem 2015; 11:302-8. [DOI: 10.1002/cmdc.201500457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/19/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Lubomir L. Vezenkov
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Clément A. Sanchez
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Virginie Bellet
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Vincent Martin
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Marie Maynadier
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Nadir Bettache
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Vincent Lisowski
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Marcel Garcia
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron (IBMM); UMR5247 CNRS; Université de Montpellier; ENSCM, Faculté de Pharmacie; 15 avenue Charles Flahault 34093 Montpellier Cedex 5 France
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Saenger Y, Magidson J, Liaw B, de Moll E, Harcharik S, Fu Y, Wassmann K, Fisher D, Kirkwood J, Oh WK, Friedlander P. Blood mRNA expression profiling predicts survival in patients treated with tremelimumab. Clin Cancer Res 2014; 20:3310-8. [PMID: 24721645 DOI: 10.1158/1078-0432.ccr-13-2906] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Tremelimumab (ticilimumab, Pfizer), is a monoclonal antibody (mAb) targeting cytotoxic T lymphocyte-associated antigen-4 (CTLA-4). Ipilimumab (Yervoy, BMS), another anti-CTLA-4 antibody, is approved by the U.S. Federal Drug Administration (FDA). Biomarkers are needed to identify the subset of patients who will achieve tumor control with CTLA-4 blockade. EXPERIMENTAL DESIGN Pretreatment peripheral blood samples from 218 patients with melanoma who were refractory to prior therapy and receiving tremelimumab in a multicenter phase II study were measured for 169 mRNA transcripts using reverse transcription polymerase chain reaction (RT-PCR). A two-class latent model yielded a risk score based on four genes that were highly predictive of survival (P < 0.001). This signature was validated in an independent population of 260 treatment-naïve patients with melanoma enrolled in a multicenter phase III study of tremelimumab. RESULTS Median follow-up was 297 days for the training population and 386 days for the test population. Expression levels of the 169 genes were closely correlated across the two populations (r = 0.9939). A four-gene model, including cathepsin D (CTSD), phopholipase A2 group VII (PLA2G7), thioredoxin reductase 1 (TXNRD1), and interleukin 1 receptor-associated kinase 3 (IRAK3), predicted survival in the test population (P = 0.001 by log-rank test). This four-gene model added to the predictive value of clinical predictors (P < 0.0001). CONCLUSIONS Expression levels of CTSD, PLA2G7, TXNRD1, and IRAK3 in peripheral blood are predictive of survival in patients with melanoma treated with tremelimumab. Blood mRNA signatures should be further explored to define patient subsets likely to benefit from immunotherapy.
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Affiliation(s)
- Yvonne Saenger
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, CanadaAuthors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - Jay Magidson
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - Bobby Liaw
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - Ellen de Moll
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - Sara Harcharik
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - Yichun Fu
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - Karl Wassmann
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - David Fisher
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - John Kirkwood
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - William K Oh
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
| | - Philip Friedlander
- Authors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, CanadaAuthors' Affiliations: Division of Hematology and Oncology, Tisch Cancer Institute, Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York; Statistical Innovations, Belmont; Department of Dermatology, Harvard Medical School, Boston, Massachusetts; Departments of Medicine, Dermatology and Translational Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; and Gene News, Ontario, Canada
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Pernemalm M, De Petris L, Branca RM, Forshed J, Kanter L, Soria JC, Girard P, Validire P, Pawitan Y, van den Oord J, Lazar V, Påhlman S, Lewensohn R, Lehtiö J. Quantitative proteomics profiling of primary lung adenocarcinoma tumors reveals functional perturbations in tumor metabolism. J Proteome Res 2013; 12:3934-43. [PMID: 23902561 DOI: 10.1021/pr4002096] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, we have analyzed human primary lung adenocarcinoma tumors using global mass spectrometry to elucidate the biological mechanisms behind relapse post surgery. In total, we identified over 3000 proteins with high confidence. Supervised multivariate analysis was used to select 132 proteins separating the prognostic groups. Based on in-depth bioinformatics analysis, we hypothesized that the tumors with poor prognosis had a higher glycolytic activity and HIF activation. By measuring the bioenergetic cellular index of the tumors, we could detect a higher dependency of glycolysis among the tumors with poor prognosis. Further, we could also detect an up-regulation of HIF1α mRNA expression in tumors with early relapse. Finally, we selected three proteins that were upregulated in the poor prognosis group (cathepsin D, ENO1, and VDAC1) to confirm that the proteins indeed originated from the tumor and not from a stromal or inflammatory component. Overall, these findings show how in-depth analysis of clinical material can lead to an increased understanding of the molecular mechanisms behind tumor progression.
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Affiliation(s)
- Maria Pernemalm
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
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Li QK, Shah P, Li Y, Aiyetan PO, Chen J, Yung R, Molena D, Gabrielson E, Askin F, Chan DW, Zhang H. Glycoproteomic analysis of bronchoalveolar lavage (BAL) fluid identifies tumor-associated glycoproteins from lung adenocarcinoma. J Proteome Res 2013; 12:3689-96. [PMID: 23802180 DOI: 10.1021/pr400274w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in eight cases of BAL fluid, as well as eight lung adenocarcinoma tissues and eight tumor-matched normal lung tissues, were analyzed using the solid-phase extraction of N-glycoprotein (SPEG), iTRAQ labeling, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Of 80 glycoproteins found in BAL specimens, 32 were identified in both cancer BAL and cancer tissues, with levels of 25 glycoproteins showing at least a 2-fold difference between cancer and benign BAL. Among them, eight glycoproteins showed greater than 2-fold elevations in cancer BAL, including Neutrophil elastase (NE), Integrin alpha-M, Cullin-4B, Napsin A, lysosome-associated membrane protein 2 (LAMP2), Cathepsin D, BPI fold-containing family B member 2, and Neutrophil gelatinase-associated lipocalin. The levels of Napsin A in cancer BAL were further verified in independently collected 39 BAL specimens using an ELISA assay. Our study demonstrates that potential protein biomarkers in BAL fluid can be detected and quantified.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21287, USA.
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