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Azimi A, Fernandez-Peñas P. Molecular Classifiers in Skin Cancers: Challenges and Promises. Cancers (Basel) 2023; 15:4463. [PMID: 37760432 PMCID: PMC10526380 DOI: 10.3390/cancers15184463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Skin cancers are common and heterogenous malignancies affecting up to two in three Australians before age 70. Despite recent developments in diagnosis and therapeutic strategies, the mortality rate and costs associated with managing patients with skin cancers remain high. The lack of well-defined clinical and histopathological features makes their diagnosis and classification difficult in some cases and the prognostication difficult in most skin cancers. Recent advancements in large-scale "omics" studies, including genomics, transcriptomics, proteomics, metabolomics and imaging-omics, have provided invaluable information about the molecular and visual landscape of skin cancers. On many occasions, it has refined tumor classification and has improved prognostication and therapeutic stratification, leading to improved patient outcomes. Therefore, this paper reviews the recent advancements in omics approaches and appraises their limitations and potential for better classification and stratification of skin cancers.
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Affiliation(s)
- Ali Azimi
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - Pablo Fernandez-Peñas
- Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Department of Dermatology, Westmead Hospital, Westmead, NSW 2145, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
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2
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Teh R, Azimi A, Pupo GM, Ali M, Mann GJ, Fernández-Peñas P. Genomic and proteomic findings in early melanoma and opportunities for early diagnosis. Exp Dermatol 2023; 32:104-116. [PMID: 36373875 DOI: 10.1111/exd.14705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/02/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Overdiagnosis of early melanoma is a significant problem. Due to subtle unique and overlapping clinical and histological criteria between pigmented lesions and the risk of mortality from melanoma, some benign pigmented lesions are diagnosed as melanoma. Although histopathology is the gold standard to diagnose melanoma, there is a demand to find alternatives that are more accurate and cost-effective. In the current "omics" era, there is gaining interest in biomarkers to help diagnose melanoma early and to further understand the mechanisms driving tumor progression. Genomic investigations have attempted to differentiate malignant melanoma from benign pigmented lesions. However, genetic biomarkers of early melanoma diagnosis have not yet proven their value in the clinical setting. Protein biomarkers may be more promising since they directly influence tissue phenotype, a result of by-products of genomic mutations, posttranslational modifications and environmental factors. Uncovering relevant protein biomarkers could increase confidence in their use as diagnostic signatures. Currently, proteomic investigations of melanoma progression from pigmented lesions are limited. Studies have previously characterised the melanoma proteome from cultured cell lines and clinical samples such as serum and tissue. This has been useful in understanding how melanoma progresses into metastasis and development of resistance to adjuvant therapies. Currently, most studies focus on metastatic melanoma to find potential drug therapy targets, prognostic factors and markers of resistance. This paper reviews recent advancements in the genomics and proteomic fields and reports potential avenues, which could help identify and differentiate melanoma from benign pigmented lesions and prevent the progression of melanoma.
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Affiliation(s)
- Rachel Teh
- Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Westmead, New South Wales, Australia.,Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Ali Azimi
- Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Westmead, New South Wales, Australia.,Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Gulietta M Pupo
- Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Westmead, New South Wales, Australia.,Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Marina Ali
- Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Westmead, New South Wales, Australia
| | - Graham J Mann
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia.,The John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Pablo Fernández-Peñas
- Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Westmead, New South Wales, Australia.,Department of Dermatology, Westmead Hospital, Westmead, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
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3
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Militaru IV, Rus AA, Munteanu CV, Manica G, Petrescu SM. New panel of biomarkers to discriminate between amelanotic and melanotic metastatic melanoma. Front Oncol 2023; 12:1061832. [PMID: 36776379 PMCID: PMC9909407 DOI: 10.3389/fonc.2022.1061832] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023] Open
Abstract
Melanoma is a form of skin cancer that can rapidly invade distant organs. A distinctive feature of melanomas is their pigmentation status, as melanin is present in most skin melanomas, whilst many metastatic tumors could become amelanotic. Besides the obvious malfunction of the key genes of the melanin pathway, the amelanotic tumors could bear a characteristic molecular signature accounting for their aggressivity. Using mass spectrometry-based proteomics we report here a distinctive panel of biomarkers for amelanotic aggressive melanoma that differ from the less invasive pigmented cells. The developed method allows the label-free quantification of proteins identified by LC-MS/MS analysis. We found a set of proteins comprising AHNAK, MYOF, ANXA1, CAPN2, ASPH, EPHA2, THBS1, TGM2, ACTN4 along with proteins involved in cell adhesion/migration (integrins, PLEC, FSCN1, FN1) that are highly expressed in amelanotic melanoma. Accompanying the down regulation of pigmentation specific proteins such as tyrosinase and TYRP1, these biomarkers are highly specific for a type of highly invasive melanoma. Interestingly, the LC-MS/MS proteomics analysis in hypoxia revealed that the abundance of this specific set of proteins found in normoxia was rather unaltered in these conditions. These biomarkers could therefore predict a metastatic behaviour for the amelanotic cells in the early stages of the tumor development and thus serve in melanoma prognostic. Applying this algorithm to related databases including melanoma samples published by independent laboratories/public databases we confirm the specificity of the newly found signatures. Overall, we begin to unravel the molecular alterations in the amelanotic melanoma and how basic proteomics offers insights into how to assess the clinical, pathological and misdiagnosis differences between the main subtypes of melanoma.
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Affiliation(s)
- Ioana V. Militaru
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Alina Adriana Rus
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Cristian V.A. Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Bucharest, Romania
| | - Georgiana Manica
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania
| | - Stefana M. Petrescu
- Department of Molecular Cell Biology, Institute of Biochemistry, Bucharest, Romania,*Correspondence: Stefana M. Petrescu,
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Lu C, Wei J. Nestin Regulates Keap1-Nrf2-HO-1-Mediated Antioxidant Responses during Stress and Malignant Hematopoiesis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1706585. [PMID: 35669731 PMCID: PMC9167119 DOI: 10.1155/2022/1706585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/20/2022]
Abstract
Objective To investigate the role of nestin in regulating Keap1-nuclear factor erythroid-2-related factor 2 (Nrf2)-heme oxygenase-1-(HO-1-) mediated antioxidant responses in stress and malignant hematopoiesis. Methods The mRNA of peripheral blood mononuclear cells was extracted from 20 leukemia patients and 20 healthy people who were hospitalized in the Hematology Department of our hospital from September 2020 to December 2021, and the mRNA levels of nestin, Keap1, Nrf2, and HO-1 were detected by real-time- (RT-) PCR. Results Compared with healthy controls, the mRNA of nestin, Keap1, Nrf2, and HO-1 in peripheral blood mononuclear cells of leukemia patients was significantly upregulated. Conclusion The occurrence and development of leukemia are closely related to nestin regulating Keap1-Nrf2-Ho-1 signal pathway. Research Significance. This study determined the effect of nestin on the biological behavior of leukemia cells and its possible mechanism and confirmed that nestin may be a marker of tumor and tumor blood vessels.
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Affiliation(s)
- Chunjuan Lu
- Department of Blood Transfusion, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, China
| | - Jin Wei
- Department of Nutrition, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, China
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5
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Schäfer MEA, Keller F, Schumacher J, Haas H, Vascotto F, Sahin U, Hafner M, Rudolf R. 3D Melanoma Cocultures as Improved Models for Nanoparticle-Mediated Delivery of RNA to Tumors. Cells 2022; 11:cells11061026. [PMID: 35326474 PMCID: PMC8946997 DOI: 10.3390/cells11061026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Cancer therapy is an emergent application for mRNA therapeutics. While in tumor immunotherapy, mRNA encoding for tumor-associated antigens is delivered to antigen-presenting cells in spleen and lymph nodes, other therapeutic options benefit from immediate delivery of mRNA nanomedicines directly to the tumor. However, tumor targeting of mRNA therapeutics is still a challenge, since, in addition to delivery of the cargo to the tumor, specifics of the targeted cell type as well as its interplay with the tumor microenvironment are crucial for successful intervention. This study investigated lipoplex nanoparticle-mediated mRNA delivery to spheroid cell culture models of melanoma. Insights into cell-type specific targeting, non-cell-autonomous effects, and penetration capacity in tumor and stroma cells of the mRNA lipoplex nanoparticles were obtained. It was shown that both coculture of different cell types as well as three-dimensional cell growth characteristics can modulate distribution and transfection efficiency of mRNA lipoplex formulations. The results demonstrate that three-dimensional coculture spheroids can provide a valuable surplus of information in comparison to adherent cells. Thus, they may represent in vitro models with enhanced predictivity for the in vivo activity of cancer nanotherapeutics.
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Affiliation(s)
- Maximilian E. A. Schäfer
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany; (M.E.A.S.); (F.K.); (M.H.)
| | - Florian Keller
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany; (M.E.A.S.); (F.K.); (M.H.)
| | - Jens Schumacher
- Biopharmaceutical New Technology (BioNTech) SE, 55131 Mainz, Germany; (J.S.); (H.H.); (U.S.)
| | - Heinrich Haas
- Biopharmaceutical New Technology (BioNTech) SE, 55131 Mainz, Germany; (J.S.); (H.H.); (U.S.)
| | - Fulvia Vascotto
- Translational Oncology (TRON), University Medical Center, Johannes Gutenberg University Mainz, 55131 Mainz, Germany;
| | - Ugur Sahin
- Biopharmaceutical New Technology (BioNTech) SE, 55131 Mainz, Germany; (J.S.); (H.H.); (U.S.)
| | - Mathias Hafner
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany; (M.E.A.S.); (F.K.); (M.H.)
- Institute of Medical Technology, Heidelberg University and Hochschule Mannheim, 68163 Mannheim, Germany
| | - Rüdiger Rudolf
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany; (M.E.A.S.); (F.K.); (M.H.)
- Institute of Medical Technology, Heidelberg University and Hochschule Mannheim, 68163 Mannheim, Germany
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Hochschule Mannheim, 68163 Mannheim, Germany
- Correspondence: ; Tel.: +49-621-292-6804
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6
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Szymańska-Chabowska A, Świątkowski F, Jankowska-Polańska B, Mazur G, Chabowski M. Nestin Expression as a Diagnostic and Prognostic Marker in Colorectal Cancer and Other Tumors. CLINICAL MEDICINE INSIGHTS-ONCOLOGY 2021; 15:11795549211038256. [PMID: 34421318 PMCID: PMC8377314 DOI: 10.1177/11795549211038256] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Lung cancer, colon cancer, breast cancer, and prostate cancer are the leading causes of death in developed countries. Many cancers display non-specific signs in the early stage of the disease, thus making early diagnosis often difficult. We focused on nestin as a new biomarker of possible clinical importance in the early diagnosis and monitoring of cancer. The expression of nestin takes place at an early stage of neural differentiation, but no expression of the nestin gene can be revealed in normal, mature adult tissues. Nestin plays an important role in the development of the central nervous system and contributes to the organization and maintenance of cell shape. Nestin was found to be a marker of microvessel density, which in turn has proven to be a reliable prognostic factor for neoplastic malignancies in patients. Nestin expression correlates with an increased aggressiveness of tumor cells. The role of nestin in cancers of the colon and rectum, liver, central nervous system, lung cancer, breast cancer, melanoma, and other cancers has been reviewed in the literature. Associations between nestin expression and prognosis or drug-resistance may help in disease management. More research is needed to understand the molecular mechanisms of nestin expression and its role in possible targeted therapy.
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Affiliation(s)
- Anna Szymańska-Chabowska
- Department of Internal Medicine, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Filip Świątkowski
- Department of Surgery, 4th Military Teaching Hospital, Wroclaw, Poland
| | - Beata Jankowska-Polańska
- Division of Nervous System Diseases, Department of Clinical Nursing, Faculty of Health Science, Wroclaw Medical University, Wroclaw, Poland
| | - Grzegorz Mazur
- Department of Internal Medicine, Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Mariusz Chabowski
- Department of Surgery, 4th Military Teaching Hospital, Wroclaw, Poland.,Division of Oncology and Palliative Care, Department of Clinical Nursing, Faculty of Health Science, Wroclaw Medical University, Wroclaw, Poland
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7
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Schäfer MEA, Klicks J, Hafner M, Rudolf R. Preparation, Drug Treatment, and Immunohistological Analysis of Tri-Culture Spheroid 3D Melanoma-Like Models. Methods Mol Biol 2021; 2265:173-183. [PMID: 33704714 DOI: 10.1007/978-1-0716-1205-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Most currently available three-dimensional melanoma models have either focused on simplicity or were optimized for physiological relevance. Accordingly, these paradigms have been either composed of malignant cells only or they were sophisticated human skin equivalents featuring multiple cell types and skin-like organization. Here, an intermediate spheroid-based assay system is presented, which uses tri-cultures of human CCD-1137Sk fibroblasts, HaCaT keratinocytes, and SK-MEL-28 melanoma cells. Being made of cell lines, these spheroids can be reliably reproduced without any special equipment using standard culture procedures, and they feature different aspects of skin and early stage melanoma. Therefore, this kind of model can be useful for lead-compound testing or addressing fundamental principles of early melanoma formation.
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Affiliation(s)
| | - Julia Klicks
- Institute of Molecular and Cell Biology, Hochschule Mannheim, Mannheim, Germany
| | - Mathias Hafner
- Institute of Molecular and Cell Biology, Hochschule Mannheim, Mannheim, Germany
| | - Rüdiger Rudolf
- Institute of Molecular and Cell Biology, Hochschule Mannheim, Mannheim, Germany.
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8
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Surman M, Kędracka-Krok S, Hoja-Łukowicz D, Jankowska U, Drożdż A, Stępień EŁ, Przybyło M. Mass Spectrometry-Based Proteomic Characterization of Cutaneous Melanoma Ectosomes Reveals the Presence of Cancer-Related Molecules. Int J Mol Sci 2020; 21:E2934. [PMID: 32331267 PMCID: PMC7215915 DOI: 10.3390/ijms21082934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 01/18/2023] Open
Abstract
Cutaneous melanoma (CM) is an aggressive type of skin cancer for which effective biomarkers are still needed. Recently, the protein content of extracellular vesicles (ectosomes and exosomes) became increasingly investigated in terms of its functional role in CM and as a source of novel biomarkers; however, the data concerning the proteome of CM-derived ectosomes is very limited. We used the shotgun nanoLC-MS/MS approach to the profile protein content of ectosomes from primary (WM115, WM793) and metastatic (WM266-4, WM1205Lu) CM cell lines. Additionally, the effect exerted by CM ectosomes on recipient cells was assessed in terms of cell proliferation (Alamar Blue assay) and migratory properties (wound healing assay). All cell lines secreted heterogeneous populations of ectosomes enriched in the common set of proteins. A total of 1507 unique proteins were identified, with many of them involved in cancer cell proliferation, migration, escape from apoptosis, epithelial-mesenchymal transition and angiogenesis. Isolated ectosomes increased proliferation and motility of recipient cells, likely due to the ectosomal transfer of different cancer-promoting molecules. Taken together, these results confirm the significant role of ectosomes in several biological processes leading to CM development and progression, and might be used as a starting point for further studies exploring their diagnostic and prognostic potential.
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Affiliation(s)
- Magdalena Surman
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland; (M.S.); (D.H.-Ł.)
| | - Sylwia Kędracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Dorota Hoja-Łukowicz
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland; (M.S.); (D.H.-Ł.)
| | - Urszula Jankowska
- Proteomics and Mass Spectrometry Core Facility, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Anna Drożdż
- Department of Medical Physics, M. Smoluchowski Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 Kraków, Poland; (A.D.); (E.Ł.S.)
| | - Ewa Ł. Stępień
- Department of Medical Physics, M. Smoluchowski Institute of Physics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-348 Kraków, Poland; (A.D.); (E.Ł.S.)
| | - Małgorzata Przybyło
- Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, 30-387 Kraków, Poland; (M.S.); (D.H.-Ł.)
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Schmitt M, Sinnberg T, Nalpas NC, Maass A, Schittek B, Macek B. Quantitative Proteomics Links the Intermediate Filament Nestin to Resistance to Targeted BRAF Inhibition in Melanoma Cells. Mol Cell Proteomics 2019; 18:1096-1109. [PMID: 30890564 PMCID: PMC6553926 DOI: 10.1074/mcp.ra119.001302] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/15/2019] [Indexed: 12/21/2022] Open
Abstract
Targeted inhibition of mutated kinases using selective MAP kinase inhibitors in malignant melanoma often results in temporary improvement of clinical symptoms followed by rapid development of resistance. To gain insights in molecular processes that govern resistance, we performed SILAC-based quantitative proteomics profiling of vemurafenib-resistant and -sensitive melanoma cells. Among downregulated proteins in vemurafenib-resistant cell lines we detected multiple proteins involved in cytoskeletal organization and signaling, including the intermediate filament nestin, which was one of the most downregulated proteins. Previous studies showed that nestin is expressed in various types of solid tumors and its abundance correlates with malignant phenotype of transformed cells. However, the role of nestin in cancer cells regarding acquired resistance is still poorly understood. We performed CRISPR/Cas9 knockout of the nestin gene (NES) in vemurafenib-sensitive cells and showed that loss of nestin leads to increased cellular proliferation and colony formation upon treatment with BRAFV600E and MEK inhibitors. Moreover, nestin depletion led to increased invasiveness and metalloproteinase activity like the phenotype of melanoma cells with acquired resistance to the BRAF inhibitor. Finally, phosphoproteome analysis revealed that nestin depletion influenced signaling through integrin and PI3K/AKT/mTOR pathways and led to increased focal adhesion kinase abundance and phosphorylation. Taken together, our results reveal that nestin is associated with acquired vemurafenib resistance in melanoma cells.
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Affiliation(s)
- Marisa Schmitt
- From the ‡Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Tobias Sinnberg
- §Center for Dermatooncology, Department of Dermatology, University of Tuebingen, Tuebingen, Germany
| | - Nicolas C Nalpas
- From the ‡Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Annika Maass
- From the ‡Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Birgit Schittek
- §Center for Dermatooncology, Department of Dermatology, University of Tuebingen, Tuebingen, Germany
| | - Boris Macek
- From the ‡Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany;
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10
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Bui L, Shen Q, Hill T, Bhuiyan SH, Barakat R, Saavedra V, Kong C, Battiste JD, Kim YT. Microchannel device for proteomic analysis of migrating cancer cells. Biomed Phys Eng Express 2018. [DOI: 10.1088/2057-1976/aacd5f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Huang R, Chen Z, He L, He N, Xi Z, Li Z, Deng Y, Zeng X. Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application. Theranostics 2017; 7:3559-3572. [PMID: 28912895 PMCID: PMC5596443 DOI: 10.7150/thno.20797] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/12/2017] [Indexed: 12/13/2022] Open
Abstract
There is a critical need for the discovery of novel biomarkers for early detection and targeted therapy of cancer, a major cause of deaths worldwide. In this respect, proteomic technologies, such as mass spectrometry (MS), enable the identification of pathologically significant proteins in various types of samples. MS is capable of high-throughput profiling of complex biological samples including blood, tissues, urine, milk, and cells. MS-assisted proteomics has contributed to the development of cancer biomarkers that may form the foundation for new clinical tests. It can also aid in elucidating the molecular mechanisms underlying cancer. In this review, we discuss MS principles and instrumentation as well as approaches in MS-based proteomics, which have been employed in the development of potential biomarkers. Furthermore, the challenges in validation of MS biomarkers for their use in clinical practice are also reviewed.
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Affiliation(s)
- Rongrong Huang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongsi Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lei He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Zhijiang Xi
- School of Medicine, Yangtze University, Jingzhou 434023, China
| | - Zhiyang Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology; Hunan University of Technology, Zhuzhou 412007, China
| | - Xin Zeng
- Nanjing Maternity and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
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12
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Hartung N, Huynh CTK, Gaudy-Marqueste C, Flavian A, Malissen N, Richard-Lallemand MA, Hubert F, Grob JJ. Study of metastatic kinetics in metastatic melanoma treated with B-RAF inhibitors: Introducing mathematical modelling of kinetics into the therapeutic decision. PLoS One 2017; 12:e0176080. [PMID: 28472075 PMCID: PMC5417482 DOI: 10.1371/journal.pone.0176080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/05/2017] [Indexed: 01/09/2023] Open
Abstract
Background Evolution of metastatic melanoma (MM) under B-RAF inhibitors (BRAFi) is unpredictable, but anticipation is crucial for therapeutic decision. Kinetics changes in metastatic growth are driven by molecular and immune events, and thus we hypothesized that they convey relevant information for decision making. Patients and methods We used a retrospective cohort of 37 MM patients treated by BRAFi only with at least 2 close CT-scans available before BRAFi, as a model to study kinetics of metastatic growth before, under and after BRAFi. All metastases (mets) were individually measured at each CT-scan. From these measurements, different measures of growth kinetics of each met and total tumor volume were computed at different time points. A historical cohort permitted to build a reference model for the expected spontaneous disease kinetics without BRAFi. All variables were included in Cox and multistate regression models for survival, to select best candidates for predicting overall survival. Results Before starting BRAFi, fast kinetics and moreover a wide range of kinetics (fast and slow growing mets in a same patient) were pejorative markers. At the first assessment after BRAFi introduction, high heterogeneity of kinetics predicted short survival, and added independent information over RECIST progression in multivariate analysis. Metastatic growth rates after BRAFi discontinuation was usually not faster than before BRAFi introduction, but they were often more heterogeneous than before. Conclusions Monitoring kinetics of different mets before and under BRAFi by repeated CT-scan provides information for predictive mathematical modelling. Disease kinetics deserves more interest
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Affiliation(s)
- Niklas Hartung
- Department of Clinical Pharmacy and Biochemistry, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Cécilia T.-K. Huynh
- Aix-Marseille Université, APHM, Dermatology and skin cancers Department, Marseille, France
| | - Caroline Gaudy-Marqueste
- Aix-Marseille Université, APHM, Dermatology and skin cancers Department, Marseille, France
- Aix-Marseille Université, UMR_S 911 CRO2, Marseille, France
- * E-mail:
| | - Antonin Flavian
- APHM, Hopital Timone, Radiology department, Marseille, France
| | - Nausicaa Malissen
- Aix-Marseille Université, APHM, Dermatology and skin cancers Department, Marseille, France
| | - Marie-Aleth Richard-Lallemand
- Aix-Marseille Université, APHM, Dermatology and skin cancers Department, Marseille, France
- Aix-Marseille Université, UMR_S 911 CRO2, Marseille, France
| | - Florence Hubert
- Aix-Marseille Université, I2M, UMR 7373, CNRS, Centrale Marseille, Marseille, France
| | - Jean-Jacques Grob
- Aix-Marseille Université, APHM, Dermatology and skin cancers Department, Marseille, France
- Aix-Marseille Université, UMR_S 911 CRO2, Marseille, France
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13
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Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KSM, Koomen JM. Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition. J Proteome Res 2016; 15:4476-4489. [PMID: 27934295 DOI: 10.1021/acs.jproteome.6b00613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Patients with BRAF V600E mutant melanoma are typically treated with targeted BRAF kinase inhibitors, such as vemurafenib and dabrafenib. Although these drugs are initially effective, they are not curative. Most of the focus to date has been upon genetic mechanisms of acquired resistance; therefore, we must better understand the global signaling adaptations that mediate escape from BRAF inhibition. In the current study, we have used activity-based protein profiling (ABPP) with ATP-analogue probes to enrich kinases and other enzyme classes that contribute to BRAF inhibitor (BRAFi) resistance in four paired isogenic BRAFi-naïve/resistant cell line models. Our analysis showed these cell line models, which also differ in their PTEN status, have considerable heterogeneity in their kinase ATP probe uptake in comparing both naïve cells and adaptations to chronic drug exposure. A number of kinases including FAK1, SLK, and TAOK2 had increased ATP probe uptake in BRAFi resistant cells, while KHS1 (M4K5) and BRAF had decreased ATP probe uptake in the BRAFi-resistant cells. Gene ontology (GO) enrichment analysis revealed BRAFi resistance is associated with a significant enhancement in ATP probe uptake in proteins implicated in cytoskeletal organization and adhesion, and decreases in ATP probe uptake in proteins associated with cell metabolic processes. The ABPP approach was able to identify key phenotypic mediators critical for each BRAFi resistant cell line. Together, these data show that common phenotypic adaptations to BRAF inhibition can be mediated through very different signaling networks, suggesting considerable redundancy within the signaling of BRAF mutant melanoma cells.
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Affiliation(s)
- Ritin Sharma
- Molecular Oncology, ‡Tumor Biology, §Cutaneous Oncology, and ∥The Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Inna Fedorenko
- Molecular Oncology, ‡Tumor Biology, §Cutaneous Oncology, and ∥The Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Paige T Spence
- Molecular Oncology, ‡Tumor Biology, §Cutaneous Oncology, and ∥The Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Vernon K Sondak
- Molecular Oncology, ‡Tumor Biology, §Cutaneous Oncology, and ∥The Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Keiran S M Smalley
- Molecular Oncology, ‡Tumor Biology, §Cutaneous Oncology, and ∥The Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - John M Koomen
- Molecular Oncology, ‡Tumor Biology, §Cutaneous Oncology, and ∥The Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612, United States
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14
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Abstract
Although the emergence of proteomics as an independent branch of science is fairly recent, within a short period of time it has contributed substantially in various disciplines. The tool of mass spectrometry has become indispensable in the analysis of complex biological samples. Clinical applications of proteomics include detection of predictive and diagnostic markers, understanding mechanism of action of drugs as well as resistance mechanisms against them and assessment of therapeutic efficacy and toxicity of drugs in patients. Here, we have summarized the major contributions of proteomics towards the study of melanoma, which is a deadly variety of skin cancer with a high mortality rate.
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Affiliation(s)
- Deepanwita Sengupta
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA; Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
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15
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Rezaul K, Gupta D, Semenova I, Ikeda K, Kraikivski P, Yu J, Cowan A, Zaliapin I, Rodionov V. Engineered Tug-of-War Between Kinesin and Dynein Controls Direction of Microtubule Based Transport In Vivo. Traffic 2016; 17:475-86. [PMID: 26843027 DOI: 10.1111/tra.12385] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 01/19/2023]
Abstract
Bidirectional transport of membrane organelles along microtubules (MTs) is driven by plus-end directed kinesins and minus-end directed dynein bound to the same cargo. Activities of opposing MT motors produce bidirectional movement of membrane organelles and cytoplasmic particles along MT transport tracks. Directionality of MT-based transport might be controlled by a protein complex that determines which motor type is active at any given moment of time, or determined by the outcome of a tug-of-war between MT motors dragging cargo organelles in opposite directions. However, evidence in support of each mechanisms of regulation is based mostly on the results of theoretical analyses or indirect experimental data. Here, we test whether the direction of movement of membrane organelles in vivo can be controlled by the tug-of-war between opposing MT motors alone, by attaching a large number of kinesin-1 motors to organelles transported by dynein to minus-ends of MTs. We find that recruitment of kinesin significantly reduces the length and velocity of minus-end-directed dynein-dependent MT runs, leading to a reversal of the overall direction of dynein-driven organelles in vivo. Therefore, in the absence of external regulators tug-of-war between opposing MT motors alone is sufficient to determine the directionality of MT transport in vivo.
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Affiliation(s)
- Karim Rezaul
- R.D.Berlin Center for Cell Analysis and Modeling, and Department of Cell Biology, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6406, USA
| | - Dipika Gupta
- R.D.Berlin Center for Cell Analysis and Modeling, and Department of Cell Biology, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6406, USA
| | - Irina Semenova
- R.D.Berlin Center for Cell Analysis and Modeling, and Department of Cell Biology, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6406, USA
| | - Kazuho Ikeda
- R.D.Berlin Center for Cell Analysis and Modeling, and Department of Cell Biology, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6406, USA.,Current address: Quantitative Biology Center, RIKEN, Osaka 565-0874, Japan
| | - Pavel Kraikivski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0406, USA
| | - Ji Yu
- R.D.Berlin Center for Cell Analysis and Modeling, and Department of Cell Biology, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6406, USA
| | - Ann Cowan
- R.D.Berlin Center for Cell Analysis and Modeling, and Department of Cell Biology, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6406, USA
| | - Ilya Zaliapin
- Department of Mathematics and Statistics, University of Nevada-Reno, Reno, NV 89557, USA
| | - Vladimir Rodionov
- R.D.Berlin Center for Cell Analysis and Modeling, and Department of Cell Biology, UConn Health, 400 Farmington Avenue, Farmington, CT 06030-6406, USA
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16
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Mittal P, Klingler-Hoffmann M, Arentz G, Zhang C, Kaur G, Oehler MK, Hoffmann P. Proteomics of endometrial cancer diagnosis, treatment, and prognosis. Proteomics Clin Appl 2015; 10:217-29. [DOI: 10.1002/prca.201500055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/13/2015] [Accepted: 11/02/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Parul Mittal
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Manuela Klingler-Hoffmann
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Georgia Arentz
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Chao Zhang
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
- Institute for Photonics and Advanced Sensing (IPAS); The University of Adelaide; Adelaide Australia
| | - Gurjeet Kaur
- Institute for Research in Molecular Medicine; Universiti Sains Malaysia; Minden Pulau Pinang Malaysia
| | - Martin K. Oehler
- Department of Gynaecological Oncology; Royal Adelaide Hospital; North Terrace Adelaide Australia
| | - Peter Hoffmann
- Adelaide Proteomics Centre; School of Biological Sciences; The University of Adelaide; Adelaide Australia
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17
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Antineoplastic effects of Rhodiola crenulata treatment on B16-F10 melanoma. Tumour Biol 2015; 36:9795-805. [DOI: 10.1007/s13277-015-3742-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/30/2015] [Indexed: 10/23/2022] Open
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18
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Comparison of five methods for direct extraction of surface proteins from Listeria monocytogenes for proteomic analysis by orbitrap mass spectrometry. J Microbiol Methods 2015; 110:54-60. [PMID: 25578509 DOI: 10.1016/j.mimet.2015.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/06/2015] [Accepted: 01/07/2015] [Indexed: 12/13/2022]
Abstract
Extracts of surface proteins, with minimal artifacts from contaminating cytosolic components, are highly desirable for investigating surface factors involved in the attachment and formation of biofilms by bacteria that are problematic in commercial food processing facilities. In this study, we compared the protein profiles of the food pathogen, Listeria monocytogenes, recovered after applying different surface protein extraction methods compiled from the literature: trypsin-enzymatic shaving with BICAM/sucrose or Tris/sucrose buffers (Tryp B+S, Tryp T+S), Tris-buffered urea (UB), lithium chloride (LiCl) and Tris-buffered urea applied with hypotonic-stressed cells (UB-Ghost), and subjected them to liquid chromatography tandem mass spectrometry and protein identification. The data indicate that the UB-Ghost extraction method provides a cleaner extract of surface proteins including the predicted (this study and the literature) or validated members (literature) from L. monocytogenes. This was determined by an accumulative lower unique peptide number exhibited by mass spectrometry for total cytoplasmic proteins among different surface extracts, with a majority of proteins demonstrating hydrophilic properties. The extracted proteins were from different functional categories and have associations with the cell surface, intermediary metabolism, information pathways, or functionally unknown proteins as suggested by in silico analyses performed by other groups (Leger and ListiList). The utilization of an optimized method for surface protein extraction should greatly facilitate identification by LC-MS/MS that could be useful to anyone working on molecular proteomics of bacterial surfaces.
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19
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Thongboonkerd V, LaBaer J, Domont GB. Recent Advances of Proteomics Applied to Human Diseases. J Proteome Res 2014; 13:4493-6. [DOI: 10.1021/pr501038g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit,
Office for Research and Development, Faculty of Medicine Siriraj Hospital,
and Center for Research in Complex Systems Science, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Joshua LaBaer
- Virginia G. Piper Center
for Personalized Diagnostics, Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85287-6401, United States
| | - Gilberto B. Domont
- Proteomics Unit, Institute
of Chemistry, Federal University of Rio de Janeiro (UFRJ), Avenida
Athos da Silveira Ramos, Rio de Janeiro, 21941-909 RJ, Brazil
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