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Oldani M, Cantone MC, Gaudenzi G, Carra S, Dicitore A, Saronni D, Borghi MO, Lombardi A, Caraglia M, Persani L, Vitale G. Exploring the multifaceted antitumor activity of axitinib in lung carcinoids. Front Endocrinol (Lausanne) 2024; 15:1433707. [PMID: 39050569 PMCID: PMC11266055 DOI: 10.3389/fendo.2024.1433707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Lung carcinoids (LCs) are a type of neuroendocrine tumor (NET) that originate in the bronchopulmonary tract. LCs account for 20-25% of all NETs and approximately 1-2% of lung cancers. Given the highly vascularized nature of NETs and their tendency to overexpress vascular growth factor receptors (VEGFR), inhibiting angiogenesis appears as a potential therapeutic target in slowing down tumor growth and spread. This study evaluated the long-term antitumor activity and related mechanisms of axitinib (AXI), a VEGFR-targeting drug, in LC cell lines. Methods Three LC cell lines (NCI-H727, UMC-11 and NCI-H835) were incubated with their respective EC50 AXI concentrations for 6 days. At the end of the incubation, FACS experiments and Western blot analyses were performed to examine changes in the cell cycle and the activation of apoptosis. Microscopy analyses were added to describe the mechanisms of senescence and mitotic catastrophe when present. Results The primary effect of AXI on LC cell lines is to arrest tumor growth through an indirect DNA damage. Notably, AXI triggers this response in diverse manners among the cell lines, such as inducing senescence or mitotic catastrophe. The drug seems to lose its efficacy when the DNA damage is mitigated, as observed in NCI-H835 cells. Conclusion The ability of AXI to affect cell viability and proliferation in LC tumor cells highlights its potential as a therapeutic agent. The role of DNA damage and the consequent activation of senescence seem to be a prerequisite for AXI to exert its function.
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Affiliation(s)
- Monica Oldani
- Laboratory of Geriatric and Oncologic Neuroendocrinology Research, IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Maria Celeste Cantone
- Laboratory of Geriatric and Oncologic Neuroendocrinology Research, IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Germano Gaudenzi
- Laboratory of Geriatric and Oncologic Neuroendocrinology Research, IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Silvia Carra
- Laboratory of Endocrine and Metabolic Research, IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Alessandra Dicitore
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Davide Saronni
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
- PhD Program in Experimental Medicine, University of Milan, Milan, Italy
| | - Maria Orietta Borghi
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Experimental Laboratory of Immuno-Rheumatology, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Angela Lombardi
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, Naples, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, Naples, Italy
- Laboratory of Molecular and Precision Oncology, Biogem Scarl, Ariano Irpino, Italy
| | - Luca Persani
- Laboratory of Endocrine and Metabolic Research, IRCCS, Istituto Auxologico Italiano, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Giovanni Vitale
- Laboratory of Geriatric and Oncologic Neuroendocrinology Research, IRCCS, Istituto Auxologico Italiano, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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Quantitative Proteomic Analysis Using Formalin-Fixed, Paraffin-Embedded (FFPE) Human Cardiac Tissue. Methods Mol Biol 2021; 2261:525-533. [PMID: 33421012 DOI: 10.1007/978-1-0716-1186-9_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Clinical tissue archives represent an invaluable source of biological information. Formalin-fixed, paraffin-embedded (FFPE) tissue can be used for retrospective investigation of biomarkers of diseases and prognosis.Recently, the number of studies using proteome profiling of samples from clinical archives has markedly increased. However, the application of conventional quantitative proteomics technologies remains a challenge mainly due to the harsh fixation process resulting in protein cross-linking and protein degradation. In the present chapter, we demonstrate a protocol for label-free proteomic analysis of FFPE tissue prepared from human cardiac autopsies. The data presented here highlight the applicability and suitability of FFPE heart tissue for understanding the molecular mechanism of cardiac injury using a proteomics approach.
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Azimzadeh O, Azizova T, Merl-Pham J, Blutke A, Moseeva M, Zubkova O, Anastasov N, Feuchtinger A, Hauck SM, Atkinson MJ, Tapio S. Chronic Occupational Exposure to Ionizing Radiation Induces Alterations in the Structure and Metabolism of the Heart: A Proteomic Analysis of Human Formalin-Fixed Paraffin-Embedded (FFPE) Cardiac Tissue. Int J Mol Sci 2020; 21:ijms21186832. [PMID: 32957660 PMCID: PMC7555548 DOI: 10.3390/ijms21186832] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 12/23/2022] Open
Abstract
Epidemiological studies on workers employed at the Mayak plutonium enrichment plant have demonstrated an association between external gamma ray exposure and an elevated risk of ischemic heart disease (IHD). In a previous study using fresh-frozen post mortem samples of the cardiac left ventricle of Mayak workers and non-irradiated controls, we observed radiation-induced alterations in the heart proteome, mainly downregulation of mitochondrial and structural proteins. As the control group available at that time was younger than the irradiated group, we could not exclude age as a confounding factor. To address this issue, we have now expanded our study to investigate additional samples using archival formalin-fixed paraffin-embedded (FFPE) tissue. Importantly, the control group studied here is older than the occupationally exposed (>500 mGy) group. Label-free quantitative proteomics analysis showed that proteins involved in the lipid metabolism, sirtuin signaling, mitochondrial function, cytoskeletal organization, and antioxidant defense were the most affected. A histopathological analysis elucidated large foci of fibrotic tissue, myocardial lipomatosis and lymphocytic infiltrations in the irradiated samples. These data highlight the suitability of FFPE material for proteomics analysis. The study confirms the previous results emphasizing the role of adverse metabolic changes in the radiation-associated IHD. Most importantly, it excludes age at the time of death as a confounding factor.
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Affiliation(s)
- Omid Azimzadeh
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
- Correspondence: ; Tel.: +49-89-3187-3887
| | - Tamara Azizova
- Southern Urals Biophysics Institute (SUBI), Russian Federation, 456780 Ozyorsk, Russia; (T.A.); (M.M.); (O.Z.)
| | - Juliane Merl-Pham
- Helmholtz Zentrum München—German Research Centre for Environmental Health, Research Unit Protein Science, 80939 Munich, Germany; (J.M.-P.); (S.M.H.)
| | - Andreas Blutke
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Research Unit Analytical Pathology, 85764 Neuherberg, Germany; (A.B.); (A.F.)
| | - Maria Moseeva
- Southern Urals Biophysics Institute (SUBI), Russian Federation, 456780 Ozyorsk, Russia; (T.A.); (M.M.); (O.Z.)
| | - Olga Zubkova
- Southern Urals Biophysics Institute (SUBI), Russian Federation, 456780 Ozyorsk, Russia; (T.A.); (M.M.); (O.Z.)
| | - Natasa Anastasov
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
| | - Annette Feuchtinger
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Research Unit Analytical Pathology, 85764 Neuherberg, Germany; (A.B.); (A.F.)
| | - Stefanie M. Hauck
- Helmholtz Zentrum München—German Research Centre for Environmental Health, Research Unit Protein Science, 80939 Munich, Germany; (J.M.-P.); (S.M.H.)
| | - Michael J. Atkinson
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
- Chair of Radiation Biology, Technical University of Munich, 81675 Munich, Germany
| | - Soile Tapio
- Helmholtz Zentrum München—German Research Centre for Environmental Health GmbH, Institute of Radiation Biology, 85764 Neuherberg, Germany; (N.A.); (M.J.A.); (S.T.)
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Herrera JA, Mallikarjun V, Rosini S, Montero MA, Lawless C, Warwood S, O’Cualain R, Knight D, Schwartz MA, Swift J. Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues. Clin Proteomics 2020; 17:24. [PMID: 32565759 PMCID: PMC7302139 DOI: 10.1186/s12014-020-09287-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Haematoxylin and eosin (H&E)-which respectively stain nuclei blue and other cellular and stromal material pink-are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterization can be achieved by laser capture microdissection coupled to mass spectrometry (LCM-MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing and H&E staining of tissues provides challenges with standard sample preparation methods for mass spectrometry, resulting in low protein yield. Here we describe a microproteomics technique to analyse H&E-stained, formalin-fixed paraffin-embedded (FFPE) tissues. METHODS Herein, we utilize heat extraction, physical disruption, and in column digestion for the analysis of H&E stained FFPE tissues. Micro-dissected morphologically normal human lung alveoli (0.082 mm3) and human lung blood vessels (0.094 mm3) from FFPE-fixed H&E-stained sections from Idiopathic Pulmonary Fibrosis (IPF) specimens (n = 3 IPF specimens) were then subject to a qualitative and then quantitative proteomics approach using BayesENproteomics. In addition, we tested the sensitivity of this method by processing and analysing a range of micro-dissected human lung blood vessel tissue volumes. RESULTS This approach yields 1252 uniquely expressed proteins (at a protein identification threshold of 3 unique peptides) with 892 differentially expressed proteins between these regions. In accord with prior knowledge, our methodology approach confirms that human lung blood vessels are enriched with smoothelin, CNN1, ITGA7, MYH11, TAGLN, and PTGIS; whereas morphologically normal human lung alveoli are enriched with cytokeratin-7, -8, -18, -19, 14, and -17. In addition, we identify a total of 137 extracellular matrix (ECM) proteins and immunohistologically validate that laminin subunit beta-1 localizes to morphologically normal human lung alveoli and tenascin localizes to human lung blood vessels. Lastly, we show that this micro-proteomics technique can be applied to tissue volumes as low as 0.0125 mm3. CONCLUSION Herein we show that our multistep sample preparation methodology of LCM-MS can identify distinct, characteristic proteomic compositions of anatomical features within complex fixed and stained tissues.
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Affiliation(s)
- Jeremy A. Herrera
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Venkatesh Mallikarjun
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Silvia Rosini
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Maria Angeles Montero
- Histopathology Department, Manchester University NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester, M23 9LT UK
| | - Craig Lawless
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Stacey Warwood
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Ronan O’Cualain
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - David Knight
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Martin A. Schwartz
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Joe Swift
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
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Ueno S, Eguchi H, Hotta F, Fukuda M, Kimura M, Yagita K, Suzuki T, Kusaka S. Microsporidial keratitis retrospectively diagnosed by ultrastructural study of formalin-fixed paraffin-embedded corneal tissue: a case report. Ann Clin Microbiol Antimicrob 2019; 18:17. [PMID: 31182106 PMCID: PMC6558824 DOI: 10.1186/s12941-019-0316-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 06/06/2019] [Indexed: 01/07/2023] Open
Abstract
Background The utility of formalin-fixed paraffin-embedded (FFPE) corneal tissue specimens for retrospective diagnosis of microsporidial keratitis was evaluated by transmission electron microscopy (TEM) analysis and the possible second case of microsporidial keratitis after Descemet stripping automated endothelial keratoplasty (DSAEK) was described. Case presentation A 68-year-old man presented with multiple crystalline opacities in the corneal stroma that progressed extremely slowly after DSAEK. Fungiflora Y staining of corneal scrapings from the affected regions revealed an oval microorganism. Topical voriconazole administration was ineffective and penetrating keratoplasty was performed. Histological and molecular analyses were carried out on the excised cornea. Ziehl–Neelsen staining revealed an acid-fast, oval organism that was visible by ultraviolet illumination after Fungiflora Y and Uvitex 2B staining, whereas periodic acid-Schiff and Grocott’s staining did not yield any significant findings. Microsporidium was detected by TEM of FFPE tissue. Nosema or Vittaforma sp. was suspected as the causative microorganism by PCR of FFPE tissue and by the fact that those species are known to cause eye infection. The corneal graft has maintained transparency at 1 year and half postoperatively. Conclusions This is the first known case of microsporidial keratitis diagnosed retrospectively by molecular and ultrastructural study of FFPE tissue, and the possible second case of microsporidial keratitis after DSAEK. Microsporidial keratitis should be considered when corneal opacity refractory to conventionally known therapy would occur after DSAEK. Our findings suggest that more microsporidial keratitis cases than have been reported to date can be identified by TEM or PCR examination of FFPE corneal specimens.
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Affiliation(s)
- Satoru Ueno
- Department of Ophthalmology, Kindai University Faculty of Medicine, 377-2, Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Hiroshi Eguchi
- Department of Ophthalmology, Kindai University Faculty of Medicine, 377-2, Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
| | - Fumika Hotta
- Department of Ophthalmology, Kindai University Faculty of Medicine, 377-2, Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Masahiko Fukuda
- Department of Ophthalmology, Kindai University Faculty of Medicine, 377-2, Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Masatomo Kimura
- Department of Pathology, Kindai University Faculty of Medicine, 377-2, Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Kenji Yagita
- Department of Parasitology, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku, Tokyo, 162-8640, Japan
| | - Takashi Suzuki
- Department of Ophthalmology, Toho University Medical Center, 6-11-1, Ohmorinishi, Ota, Tokyo, 143-8541, Japan
| | - Shunji Kusaka
- Department of Ophthalmology, Kindai University Faculty of Medicine, 377-2, Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
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Effects of KEAP1 Silencing on the Regulation of NRF2 Activity in Neuroendocrine Lung Tumors. Int J Mol Sci 2019; 20:ijms20102531. [PMID: 31126053 PMCID: PMC6566555 DOI: 10.3390/ijms20102531] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/09/2023] Open
Abstract
Background. The KEAP1/NRF2 pathway has been widely investigated in tumors since it was implicated in cancer cells survival and therapies resistance. In lung tumors the deregulation of this pathway is mainly related to point mutations of KEAP1 and NFE2L2 genes and KEAP1 promoter hypermethylation, but these two genes have been rarely investigated in low/intermediate grade neuroendocrine tumors of the lung. Methods. The effects of KEAP1 silencing on NRF2 activity was investigated in H720 and H727 carcinoid cell lines and results were compared with those obtained by molecular profiling of KEAP1 and NFE2L2 in a collection of 47 lung carcinoids. The correlation between methylation and transcript levels was assessed by 5-aza-dC treatment. Results. We demonstrated that in carcinoid cell lines, the KEAP1 silencing induces an upregulation of NRF2 and some of its targets and that there is a direct correlation between KEAP1 methylation and its mRNA levels. A KEAP1 hypermethylation and Loss of Heterozygosity at KEAP1 gene locus was also observed in nearly half of lung carcinoids. Conclusions. This is the first study that has described the effects of KEAP1 silencing on the regulation of NRF2 activity in lung carcinoids cells. The epigenetic deregulation of the KEAP1/NRF2 by a KEAP1 promoter hypermethylation system appears to be a frequent event in lung carcinoids.
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Jia X, Chen C, Chen L, Yu C, Kondo T. Decorin as a prognostic biomarker in patients with malignant peripheral nerve sheath tumors. Oncol Lett 2019; 17:3517-3522. [PMID: 30867792 DOI: 10.3892/ol.2019.9959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 12/04/2018] [Indexed: 01/30/2023] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft-tissue sarcomas. The prognosis of MPNSTs has been reported to differ among previous studies. However, there have been a number of reported prognostic biomarkers associated with MPNSTs. In the present study, a proteomics study was performed to discover the differential protein expression in patients with MPSNTs with different prognoses. The clinical data of 30 primary extremities of patients with MPNSTs, who underwent surgery at the Department of Hand Surgery, Huashan Hospital, Fudan University between January 2002 and December 2011, were acquired. A total of 16 patients succumbed to their diseases within 5 years, whereas 14 patients were disease-free for >5 years. Samples from the 9 patients who succumbed within 2 years were assigned to Group D, while samples from the 8 patients who were continuously disease-free for >5 years following diagnosis were assigned to Group L for the proteomics study. Label-free quantitative proteomics and mass spectrometry were performed to filtrate differential protein in patients with MPSNTs with different prognoses. Decorin was filtrated as a differential protein of note. The expression level of decorin was significantly lower in Group D compared with that in Group L (D/L=0.0948; P=0.0004). The result was verified by immunohistochemical staining in the 30 primary extremities of patients with MPNSTs. The 5-year survival rate of patients with positive expression of decorin was 78.57%, while the 5-year survival rate of patients negative for decorin expression was 18.75% (P=0.0014). Overall, a high level of decorin indicted a better prognosis in patients with MPNSTs. With further investigation, decorin may be a reliable prognostic biomarker for MPNSTs.
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Affiliation(s)
- Xiaotian Jia
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200040, P.R. China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200040, P.R. China
| | - Chao Chen
- Department of Gynecology and Obstetrics, Putuo District Center Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200062, P.R. China
| | - Lin Chen
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200040, P.R. China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200040, P.R. China
| | - Cong Yu
- Department of Hand Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China.,Key Laboratory of Hand Reconstruction, Ministry of Health, Shanghai 200040, P.R. China.,Shanghai Key Laboratory of Peripheral Nerve and Microsurgery, Shanghai 200040, P.R. China
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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Fujii K, Miyata Y, Takahashi I, Koizumi H, Saji H, Hoshikawa M, Takagi M, Nishimura T, Nakamura H. Differential Proteomic Analysis between Small Cell Lung Carcinoma (SCLC) and Pulmonary Carcinoid Tumors Reveals Molecular Signatures for Malignancy in Lung Cancer. Proteomics Clin Appl 2018; 12:e1800015. [PMID: 29888431 DOI: 10.1002/prca.201800015] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/10/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE The molecular underpinnings that may prognosticate survival and increase our understanding of tumor development and progression are still poorly understood. This study aimed to define the molecular signatures for malignancy in small cell lung carcinoma (SCLC), which is known for its highly aggressive clinical features and poor prognosis. EXPERIMENTAL DESIGN Using clinical specimens, the authors perform a comparative proteomic analysis of high-grade SCLCs and low-grade pulmonary carcinoid tumors (PCTs), both of which are types of neuroendocrine tumors. A label-free LC-MS-based quantitative proteomic analysis is applied to tumor cells laser-microdissected from their formalin-fixed paraffin-embedded (FFPE) tissues obtained from six patients each. RESULTS Overall, 1991 proteins are identified from tumor cells in the FFPE tissues. Through the protein-protein interaction network analysis of 201 proteins significantly, the authors find that SCLC is functionally characterized by activation of molecular pathways for spliceosome, RNA transport, and DNA replication and cell cycle. Particularly, 11 proteins involved in tumor proliferation (MCM2, 4, 6, 7, and MSH2), metastasis (RCC2, CORO1C, CHD4, and IPO9), and cancer metabolism (PHGDH and TYMP) are identified as SCLC-specific proteins. Furthermore, their prognostic significances are demonstrated by online Kaplan-Meier survival analysis. CONCLUSIONS AND CLINICAL RELEVANCE These clinical tissue proteomic approach for SCLC reveals the proteins associated with aggressiveness and poor prognosis. The identified SCLC-specific proteins represent potential therapeutic targets. Moreover, MCMs and PHGDH can be poor prognostic factors for lung cancer.
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Affiliation(s)
- Kiyonaga Fujii
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Japan
| | | | | | - Hirotaka Koizumi
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Masahiro Hoshikawa
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Masayuki Takagi
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Haruhiko Nakamura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Japan.,Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
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Modlin IM, Kidd M, Filosso PL, Roffinella M, Lewczuk A, Cwikla J, Bodei L, Kolasinska-Cwikla A, Chung KM, Tesselaar ME, Drozdov IA. Molecular strategies in the management of bronchopulmonary and thymic neuroendocrine neoplasms. J Thorac Dis 2017; 9:S1458-S1473. [PMID: 29201449 DOI: 10.21037/jtd.2017.03.82] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thoracic NETs [bronchopulmonary NETs (BPNETs) and thymic NETs (TNET)] share a common anatomic primary location, likely a common cell of origin, the "Kulchitsky cell" and presumably, a common etiopathogenesis. Although they are similarly grouped into well-differentiated [typical carcinoids (TC) and atypical carcinoids (AC)] and poorly differentiated neoplasms and both express somatostatin receptors, they exhibit a wide variation in clinical behavior. TNETs are more aggressive, are frequently metastatic, and have a lower 5-year survival rate (~50% vs. ~80%) than BPNETs. They are typically symptomatic, most often secreting ACTH (40% of tumors) but both tumor groups share secretion of common biomarkers including chromogranin A and 5-HIAA. Consistently effective and accurate circulating biomarkers are, however, currently unavailable. Surgery is the primary therapeutic tool for both BPNET and TNETs but there remains little consensus about later interventions e.g., targeted therapy, or how these can be monitored. Genetic analyses have identified different topographies (e.g., significant alterations in chromatin and epigenetic remodeling in BPNETs versus frequent chromosomal abnormalities in TNETs) but there is an absence of clinically actionable mutations in both tumor groups. Liquid biopsies, tools that can measure neoplastic signatures in peripheral blood, can potentially be leveraged to detect disease early i.e., recurrence, predict tumors that may respond to specific therapies and serve as real-time monitors for treatment responses. Recent studies have identified that mRNA transcript analysis in blood effectively identifies both BPNET and TNETs. The clinical utility of this gene expression assay includes use as a diagnostic, confirmation of completeness of surgical resection and use as a molecular management tool to monitor efficacy of PRRT and other therapeutic strategies.
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Affiliation(s)
| | - Mark Kidd
- Wren Laboratories, Branford, CT, USA
| | | | | | | | - Jaroslaw Cwikla
- The Faculty of Medical Sciences, University of Warmia and Mazury, Olsztyn, Poland
| | - Lisa Bodei
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Broeckx V, Boonen K, Pringels L, Sagaert X, Prenen H, Landuyt B, Schoofs L, Maes E. Comparison of multiple protein extraction buffers for GeLC-MS/MS proteomic analysis of liver and colon formalin-fixed, paraffin-embedded tissues. MOLECULAR BIOSYSTEMS 2016; 12:553-65. [PMID: 26676081 DOI: 10.1039/c5mb00670h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a potential valuable source of samples for clinical research. Since these specimens are banked in hospital archives, large cohorts of samples can be collected in short periods of time which can all be linked with a patients' clinical history. Therefore, the use of FFPE tissue in protein biomarker discovery studies gains interest. However, despite the growing number of FFPE proteome studies in the literature, there is a lack of a FFPE proteomics standard operating procedure (SOP). One of the challenging steps in the development of such a SOP is the ability to obtain an efficient and repeatable extraction of full length FFPE proteins. In this study, the protein extraction efficiency of eight protein extraction buffers is critically compared with GeLC-MS/MS (1D gel electrophoresis followed by in-gel digestion and LC-MS/MS). The data variation caused by using these extraction buffers was investigated since the variation is a very important aspect when using FFPE tissue as a source for biomarker detection. In addition, a qualitative comparison was made between the protein extraction efficiency and repeatability for FFPE tissue and fresh frozen tissue.
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Affiliation(s)
- Valérie Broeckx
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Kurt Boonen
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Lentel Pringels
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Xavier Sagaert
- Centre for Translational Cell and Tissue Research, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Hans Prenen
- Department of Gastro-Enterology, Digestive Oncology Unit, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Bart Landuyt
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Liliane Schoofs
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Evelyne Maes
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium and Centre for Proteomics, University of Antwerp/Flemish Institute for Technological Research (VITO), Groenenborgerlaan 171, 2020 Antwerp, Belgium
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Pisano M, Palomba A, Tanca A, Pagnozzi D, Uzzau S, Addis MF, Dettori MA, Fabbri D, Palmieri G, Rozzo C. Protein expression changes induced in a malignant melanoma cell line by the curcumin analogue compound D6. BMC Cancer 2016; 16:317. [PMID: 27192978 PMCID: PMC4870815 DOI: 10.1186/s12885-016-2362-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/13/2016] [Indexed: 01/09/2023] Open
Abstract
Background We have previously demonstrated that the hydroxylated biphenyl compound D6 (3E,3′E)-4,4′-(5,5′,6,6′-tetramethoxy-[1,1′-biphenyl]-3,3′-diyl)bis(but-3-en-2-one), a structural analogue of curcumin, exerts a strong antitumor activity on melanoma cells both in vitro and in vivo. Although the mechanism of action of D6 is yet to be clarified, this compound is thought to inhibit cancer cell growth by arresting the cell cycle in G2/M phase, and to induce apoptosis through the mitochondrial intrinsic pathway. To investigate the changes in protein expression induced by exposure of melanoma cells to D6, a differential proteomic study was carried out on D6-treated and untreated primary melanoma LB24Dagi cells. Methods Proteins were fractionated by SDS-PAGE and subjected to in gel digestion. The peptide mixtures were analyzed by liquid chromatography coupled with tandem mass spectrometry. Proteins were identified and quantified using database search and spectral counting. Proteomic data were finally uploaded into the Ingenuity Pathway Analysis software to find significantly modulated networks and pathways. Results Analysis of the differentially expressed protein profiles revealed the activation of a strong cellular stress response, with overexpression of several HSPs and stimulation of ubiquitin-proteasome pathways. These were accompanied by a decrease of protein synthesis, evidenced by downregulation of proteins involved in mRNA processing and translation. These findings are consistent with our previous results on gene expression profiling in melanoma cells treated with D6. Conclusions Our findings confirm that the curcumin analogue D6 triggers a strong stress response in melanoma cells, turning down majority of cell functions and finally driving cells to apoptosis. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2362-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Pisano
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Antonio Palomba
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy.,Biosistema Scrl, Sassari, Italy
| | - Alessandro Tanca
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy
| | - Daniela Pagnozzi
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy
| | - Sergio Uzzau
- Proteomics Laboratory, Porto Conte Ricerche, Tramariglio, Alghero, Italy
| | | | - Maria Antonietta Dettori
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Davide Fabbri
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy
| | - Carla Rozzo
- Institute of Biomolecular Chemistry, National Research Council of Italy, Traversa la Crucca, 3, 07100, Sassari, Italy.
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Investigation of HER2 expression in canine mammary tumors by antibody-based, transcriptomic and mass spectrometry analysis: is the dog a suitable animal model for human breast cancer? Tumour Biol 2015; 36:9083-91. [PMID: 26088453 DOI: 10.1007/s13277-015-3661-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/09/2015] [Indexed: 11/27/2022] Open
Abstract
Canine mammary tumors (CMTs) share many features with human breast cancer (HBC), specifically concerning cancer-related pathways. Although the human epidermal growth factor receptor 2 (HER2) plays a significant role as a therapeutic and prognostic biomarker in HBC, its relevance in the pathogenesis and prognosis of CMT is still controversial. The aim of this study was to investigate HER2 expression in canine mammary hyperplasic and neoplastic tissues as well as to evaluate the specificity of the most commonly used polyclonal anti HER2 antibody by multiple molecular approaches. HER2 protein and RNA expression were determined by immunohistochemistry (IHC) and by quantitative real-time (qRT) PCR. A strong cell membrane associated with non-specific cytoplasmic staining was observed in 22% of carcinomas by IHC. Adenomas and carcinomas exhibited a significantly higher HER2 mRNA expression when compared to normal mammary glands, although no significant difference between benign and malignant tumors was noticed by qRT-PCR. The IHC results suggest a lack of specificity of the FDA-approved antibody in CMT samples as further demonstrated by Western immunoblotting (WB) and reverse phase protein arrays (RPPA). Furthemore, HER2 was not detected by mass spectrometry (MS) in a protein-expressing carcinoma at the IHC investigation. This study highlights that caution needs to be used when trying to translate from human to veterinary medicine information concerning cancer-related biomarkers and pathways. Further investigations are necessary to carefully assess the diagnostic and biological role specifically exerted by HER2 in CMTs and the use of canine mammary tumors as a model of HER2 over-expressing breast cancer.
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Pisanu S, Pagnozzi D, Pes M, Pirisi A, Roggio T, Uzzau S, Addis MF. Differences in the peptide profile of raw and pasteurised ovine milk cheese and implications for its bioactive potential. Int Dairy J 2015. [DOI: 10.1016/j.idairyj.2014.10.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Righi L, Volante M, Rapa I, Vatrano S, Pelosi G, Papotti M. Therapeutic biomarkers in lung neuroendocrine neoplasia. Endocr Pathol 2014; 25:371-7. [PMID: 25252622 DOI: 10.1007/s12022-014-9335-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The well-known classification of neuroendocrine neoplasms of the lung into four major subtypes (including typical and atypical carcinoids and small- and large-cell neuroendocrine carcinomas) has a proven prognostic validity but only partially helps to predict the response to specific therapies. Therapeutic biomarkers are incompletely known and include morphological, immunophenotypic, and molecular markers. Morphology alone has no specific predictive role, nor has any immunophenotypic marker been proven to bear predictive implications. Ki67 is a relevant prognostic marker and can indirectly predict response to chemotherapy, when levels are extremely high in high-grade neuroendocrine (NE) carcinomas. The expression of somatostatin receptors, especially of the type 2A, has been shown to predict response to somatostatin analog treatments, paralleling the information derived from octreotide scintigraphy. mTOR pathway is targeted by specific inhibitors, but the exact cellular molecules predicting response are still to be defined. It seems that high levels of phosphorylated forms of mTOR and of its downstream factor S6K are associated to a better response to rapalogs in experimental models. Data from gene expression profiling and mutational analyses are currently emerging, providing a more detailed map of different molecular activation pathways, potentially leading to a more accurate molecular classification of lung NE tumors as well as to the discovery of new therapeutic targets. The combination of mutational profiles with those of upregulated or downregulated genes also by gene gains or losses may ultimately provide a better characterization of NE tumor histological types in terms of response to specific chemotherapy or biotherapy.
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Affiliation(s)
- Luisella Righi
- Department of Oncology, University of Turin at San Luigi Hospital, Regione Gonzole 10, 10043, Orbassano, Turin, Italy
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Abstract
INTRODUCTION Small-cell lung cancer (SCLC) is the most aggressive subtype of lung cancer, with no early detection strategy or targeted therapy currently available. We hypothesized that difference gel electrophoresis (DIGE) may identify membrane-associated proteins (MAPs) specific to SCLC, advance our understanding of SCLC biology, and discover new biomarkers of SCLC. METHODS MAP lysates were prepared from three SCLCs, three non-small-cell lung cancers, and three immortalized normal bronchial epithelial cell lines and coanalyzed by DIGE. Subsequent protein identification was performed by mass spectrometry. Proteins were submitted to Ingenuity Pathway Analysis. Candidate biomarkers were validated by Western blotting (WB) and immunohistochemistry (IHC). RESULTS Principal component analysis on the global DIGE data set demonstrated that the four replicates derived from each of the nine cell lines clustered closely, as did samples within the same histological group. One hundred thirty-seven proteins were differentially expressed in SCLC compared with non-small-cell lung cancer and immortalized normal bronchial epithelial cells. These proteins were overrepresented in cellular/tissue morphology networks. Dihydropyrimidinase-related protein 2, guanine nucleotide-binding protein alpha-q, laminin receptor 1, pontin, and stathmin 1 were selected as candidate biomarkers among MAPs overexpressed in SCLC. Overexpression of all candidates but RSSA in SCLC was verified by WB and/or IHC on tissue microarrays. These proteins were significantly associated with SCLC histology and survival in univariables analyses. CONCLUSION DIGE analysis of a membrane-associated subproteome discovered overexpression of dihydropyrimidinase-related protein 2, guanine nucleotide-binding protein alpha-q, RUVB1, and stathmin 1 in SCLC. Results were verified by WB and/or IHC in primary tumors, suggesting that investigating their functional relevance in SCLC progression is warranted. Association with survival requires further validation in larger clinical data sets.
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Gustafsson OJR, Arentz G, Hoffmann P. Proteomic developments in the analysis of formalin-fixed tissue. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:559-80. [PMID: 25315853 DOI: 10.1016/j.bbapap.2014.10.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/22/2014] [Accepted: 10/06/2014] [Indexed: 02/07/2023]
Abstract
Retrospective proteomic studies, including those which aim to elucidate the molecular mechanisms driving cancer, require the assembly and characterization of substantial patient tissue cohorts. The difficulty of maintaining and accessing native tissue archives has prompted the development of methods to access archives of formalin-fixed tissue. Formalin-fixed tissue archives, complete with patient meta data, have accumulated for decades, presenting an invaluable resource for these retrospective studies. This review presents the current knowledge concerning formalin-fixed tissue, with descriptions of the mechanisms of formalin fixation, protein extraction, top-down proteomics, bottom-up proteomics, quantitative proteomics, phospho- and glycoproteomics as well as imaging mass spectrometry. Particular attention has been given to the inclusion of proteomic investigations of archived tumour tissue. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Ove J R Gustafsson
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005
| | - Georgia Arentz
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005.
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Ghisaura S, Anedda R, Pagnozzi D, Biosa G, Spada S, Bonaglini E, Cappuccinelli R, Roggio T, Uzzau S, Addis MF. Impact of three commercial feed formulations on farmed gilthead sea bream (Sparus aurata, L.) metabolism as inferred from liver and blood serum proteomics. Proteome Sci 2014; 12:44. [PMID: 25342931 PMCID: PMC4200174 DOI: 10.1186/s12953-014-0044-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022] Open
Abstract
Background The zootechnical performance of three different commercial feeds and their impact on liver and serum proteins of gilthead sea bream (Sparus aurata, L.) were assessed in a 12 week feeding trial. The three feeds, named A, B, and C, were subjected to lipid and protein characterization by gas chromatography (GC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively. Results Feed B was higher in fish-derived lipids and proteins, while feeds C and A were higher in vegetable components, although the largest proportion of feed C proteins was represented by pig hemoglobin. According to biometric measurements, the feeds had significantly different impacts on fish growth, producing a higher average weight gain and a lower liver somatic index in feed B over feeds A and C, respectively. 2D DIGE/MS analysis of liver tissue and Ingenuity pathways analysis (IPA) highlighted differential changes in proteins involved in key metabolic pathways of liver, spanning carbohydrate, lipid, protein, and oxidative metabolism. In addition, serum proteomics revealed interesting changes in apolipoproteins, transferrin, warm temperature acclimation-related 65 kDa protein (Wap65), fibrinogen, F-type lectin, and alpha-1-antitrypsin. Conclusions This study highlights the contribution of proteomics for understanding and improving the metabolic compatibility of feeds for marine aquaculture, and opens new perspectives for its monitoring with serological tests. Electronic supplementary material The online version of this article (doi:10.1186/s12953-014-0044-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefania Ghisaura
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Roberto Anedda
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Grazia Biosa
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Simona Spada
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Elia Bonaglini
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Roberto Cappuccinelli
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Tonina Roggio
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
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Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev Mol Diagn 2014; 12:343-59. [DOI: 10.1586/erm.12.31] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Giusti L, Lucacchini A. Proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2013; 10:165-77. [PMID: 23573783 DOI: 10.1586/epr.13.3] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a valuable informational resource of histologically characterized specimens for proteomic studies. In this article, the authors review the advancement performed in the field of FFPE proteomics focusing on formaldehyde treatment and on strategies addressed to obtain the best recovery in the protein/peptide extraction. A variety of approaches have been used to characterize protein tissue extracts, and many efforts have been performed demonstrating the comparability between fresh/frozen and FFPE proteomes. Finally, the authors report and discuss the large numbers of works aimed at developing new strategies and sophisticated platforms in the analysis of FFPE samples to validate known potential biomarkers and to discover new ones.
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Affiliation(s)
- Laura Giusti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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Tanca A, Biosa G, Pagnozzi D, Addis MF, Uzzau S. Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome. Proteomics 2013; 13:2597-607. [PMID: 23784971 DOI: 10.1002/pmic.201200478] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 04/09/2013] [Accepted: 05/28/2013] [Indexed: 11/06/2022]
Abstract
This work presents a comparative evaluation of several detergent-based sample preparation workflows for the MS-based analysis of bacterial proteomes, performed using the model organism Escherichia coli. Initially, RapiGest- and SDS-based buffers were compared for their protein extraction efficiency and quality of the MS data generated. As a result, SDS performed best in terms of total protein yields and overall number of MS identifications, mainly due to a higher efficiency in extracting high molecular weight (MW) and membrane proteins, while RapiGest led to an enrichment in periplasmic and fimbrial proteins. Then, SDS extracts underwent five different MS sample preparation workflows, including: detergent removal by spin columns followed by in-solution digestion (SC), protein precipitation followed by in-solution digestion in ammonium bicarbonate or urea buffer, filter-aided sample preparation (FASP), and 1DE separation followed by in-gel digestion. On the whole, about 1000 proteins were identified upon LC-MS/MS analysis of all preparations (>1100 with the SC workflow), with FASP producing more identified peptides and a higher mean sequence coverage. Each protocol exhibited specific behaviors in terms of MW, hydrophobicity, and subcellular localization distribution of the identified proteins; a comparative assessment of the different outputs is presented.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, Tramariglio, Alghero, Italy; Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
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Babudieri S, Soddu A, Nieddu P, Tanca A, Madeddu G, Addis M, Pagnozzi D, Cossu-Rocca P, Massarelli G, Dore M, Uzzau S, Mura M. Proteomic characterization of hepatitis C eradication: Enzyme switch in the healing liver. J Clin Virol 2013; 57:274-8. [DOI: 10.1016/j.jcv.2013.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/23/2013] [Accepted: 03/02/2013] [Indexed: 12/13/2022]
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Pastor MD, Nogal A, Molina-Pinelo S, Carnero A, Paz-Ares L. Proteomic biomarkers in lung cancer. Clin Transl Oncol 2013; 15:671-82. [DOI: 10.1007/s12094-013-1034-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/25/2013] [Indexed: 12/12/2022]
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Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 2013; 45:205-18. [PMID: 23592010 DOI: 10.1007/s00726-013-1494-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a real treasure for retrospective analysis considering the amount of samples present in hospital archives, combined with pathological, clinical, and outcome information available for every sample. Although unlocking the proteome of these tissues is still a challenge, new approaches are being developed. In this review, we summarize the different mass spectrometry platforms that are used in human clinical studies to unravel the FFPE proteome. The different ways of extracting crosslinked proteins and the analytical strategies are pointed out. Also, the pitfalls and challenges concerning the quality of FFPE proteomic approaches are depicted. We also evaluated the potential of these analytical methods for future clinical FFPE proteomics applications.
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Craven RA, Cairns DA, Zougman A, Harnden P, Selby PJ, Banks RE. Proteomic analysis of formalin-fixed paraffin-embedded renal tissue samples by label-free MS: assessment of overall technical variability and the impact of block age. Proteomics Clin Appl 2013; 7:273-82. [PMID: 23027403 DOI: 10.1002/prca.201200065] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/04/2012] [Accepted: 09/12/2012] [Indexed: 01/17/2023]
Abstract
PURPOSE Protein profiling of formalin-fixed paraffin-embedded (FFPE) tissues has enormous potential for the discovery and validation of disease biomarkers. The aim of this study was to systematically characterize the effect of length of time of storage of such tissue blocks in pathology archives on the quality of data produced using label-free MS. EXPERIMENTAL DESIGN Normal kidney and clear cell renal cell carcinoma tissues routinely collected up to 10 years prior to analysis were profiled using LC-MS/MS and the data analyzed using MaxQuant. Protein identities and quantification data were analyzed to examine differences between tissue blocks of different ages and assess the impact of technical and biological variability. RESULTS An average of over 2000 proteins was seen in each sample with good reproducibility in terms of proteins identified and quantification for normal kidney tissue, with no significant effect of block age. Greater biological variability was apparent in the renal cell carcinoma tissue, possibly reflecting disease heterogeneity, but again there was good correlation between technical replicates and no significant effect of block age. CONCLUSIONS AND CLINICAL RELEVANCE These results indicate that archival storage time does not have a detrimental effect on protein profiling of FFPE tissues, supporting the use of such tissues in biomarker discovery studies.
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Affiliation(s)
- Rachel A Craven
- Cancer Research UK Centre,, Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, UK
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Pan S, Brentnall TA, Kelly K, Chen R. Tissue proteomics in pancreatic cancer study: discovery, emerging technologies, and challenges. Proteomics 2013; 13:710-21. [PMID: 23125171 DOI: 10.1002/pmic.201200319] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/22/2022]
Abstract
Pancreatic cancer is a highly lethal disease that is difficult to diagnose and treat. The advances in proteomics technology, especially quantitative proteomics, have stimulated a great interest in applying this technology for pancreatic cancer study. A variety of tissue proteomics approaches have been applied to investigate pancreatic cancer and the associated diseases. These studies were carried out with various goals, aiming to better understand the molecular mechanisms underlying pancreatic tumorigenesis, to improve therapeutic treatment and to identify cancer associated protein signatures, signaling events as well as interactions between cancer cells and tumor microenvironment. Here, we provide an overview on the tissue proteomics studies of pancreatic cancer reported in the past few years in light of discovery and technology development.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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Comparability of differential proteomics data generated from paired archival fresh-frozen and formalin-fixed samples by GeLC-MS/MS and spectral counting. J Proteomics 2012; 77:561-76. [PMID: 23043969 DOI: 10.1016/j.jprot.2012.09.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/17/2012] [Accepted: 09/22/2012] [Indexed: 11/22/2022]
Abstract
In this study, a Veterinary Department repository composed by paired formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FrFr) sets of the same tissues, routinely archived in the typical conditions of a clinical setting, was exploited to perform a comparative evaluation of the results generated by GeLC-MS/MS (1-DE followed by in-gel digestion and LC-MS/MS) and spectral counting with the two types of archival samples. Therefore, two parallel differential proteomic studies were performed using 3 canine mammary carcinomas and 3 normal controls in a paired fashion (6 FrFr and 6 FFPE in total). As a result, the FrFr and FFPE differential proteomic datasets exhibited fair consistency in differential expression trends, according to protein molecular function, cellular localization, networks, and pathways. However, FFPE samples were globally slightly less informative, especially concerning the high-MW subproteome. As a further investigation, new insights into the molecular aspects of protein fixation and retrieval were obtained. In conclusion, archival FFPE samples can be reliably used for differential proteomics studies employing a spectral counting GeLC-MS/MS approach, although some typical biases need to be taken into account, and FrFr specimens (when available) should still be considered as the gold standard for clinical proteomics.
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Magdeldin S, Yamamoto T. Toward deciphering proteomes of formalin-fixed paraffin-embedded (FFPE) tissues. Proteomics 2012; 12:1045-58. [PMID: 22318899 PMCID: PMC3561704 DOI: 10.1002/pmic.201100550] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens comprise a potentially valuable resource for both prospective and retrospective biomarker discovery. Unlocking the proteomic profile of clinicopathological FFPE tissues is a critically essential step for annotating clinical findings and predicting biomarkers for ultimate disease prognosis and therapeutic follow-up.
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Affiliation(s)
- Sameh Magdeldin
- Department of Structural Pathology Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
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Classification of the four main types of lung cancer using a microRNA-based diagnostic assay. J Mol Diagn 2012; 14:510-7. [PMID: 22749746 DOI: 10.1016/j.jmoldx.2012.03.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 03/18/2012] [Accepted: 03/29/2012] [Indexed: 01/27/2023] Open
Abstract
For patients with primary lung cancer, accurate determination of the tumor type significantly influences treatment decisions. However, techniques and methods for lung cancer typing lack standardization. In particular, owing to limited tumor sample amounts and the poor quality of some samples, the classification of primary lung cancers using small preoperative biopsy specimens presents a diagnostic challenge using current tools. We previously described a microRNA-based assay (miRview squamous; Rosetta Genomics Ltd., Rehovot, Israel) that accurately differentiates between squamous and nonsquamous non-small cell lung cancer. Herein, we describe the development and validation of an assay that differentiates between the four main types of lung cancer: squamous cell carcinoma, nonsquamous non-small cell lung cancer, carcinoid, and small cell carcinoma. The assay, miRview lung (Rosetta Genomics Ltd.), is based on the expression levels of eight microRNAs, measured using a sensitive quantitative RT-PCR platform. It was validated on an independent set of 451 samples, more than half of which were preoperative cytologic samples (fine-needle aspiration and bronchial brushing and washing). The assay returned a result for more than 90% of the samples with overall accuracy of 94% (95% CI, 91% to 96%), with similar performance observed in pathologic and cytologic samples. Thus, miRview lung is a simple and reliable diagnostic assay that offers an accurate and standardized classification tool for primary lung cancer using pathologic and cytologic samples.
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Tanca A, Addis MF, Simula MP, Pagnozzi D, Biosa G, Pisanu S, Garziera M, Cannizzaro R, Canzonieri V, De Re V, Uzzau S. Evaluation of the suitability of archival Bouin-fixed paraffin-embedded tissue specimens to proteomic investigation. Electrophoresis 2012; 33:1375-84. [DOI: 10.1002/elps.201200026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Alessandro Tanca
- Proteomics Laboratory; Porto Conte Ricerche Srl; Tramariglio; Alghero; Italy
| | - Maria Filippa Addis
- Proteomics Laboratory; Porto Conte Ricerche Srl; Tramariglio; Alghero; Italy
| | - Maria Paola Simula
- Experimental and Clinical Pharmacology Unit; CRO Centro di Riferimento Oncologico; IRCCS National Cancer Institute; Aviano; PN; Italy
| | - Daniela Pagnozzi
- Proteomics Laboratory; Porto Conte Ricerche Srl; Tramariglio; Alghero; Italy
| | - Grazia Biosa
- Proteomics Laboratory; Porto Conte Ricerche Srl; Tramariglio; Alghero; Italy
| | - Salvatore Pisanu
- Proteomics Laboratory; Porto Conte Ricerche Srl; Tramariglio; Alghero; Italy
| | - Marica Garziera
- Experimental and Clinical Pharmacology Unit; CRO Centro di Riferimento Oncologico; IRCCS National Cancer Institute; Aviano; PN; Italy
| | - Renato Cannizzaro
- Gastroenterology; CRO Centro di Riferimento Oncologico; IRCCS National Cancer Institute; Aviano; PN; Italy
| | - Vincenzo Canzonieri
- Pathology; CRO Centro di Riferimento Oncologico; IRCCS National Cancer Institute; Aviano; PN; Italy
| | - Valli De Re
- Experimental and Clinical Pharmacology Unit; CRO Centro di Riferimento Oncologico; IRCCS National Cancer Institute; Aviano; PN; Italy
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Klockenbusch C, O'Hara JE, Kast J. Advancing formaldehyde cross-linking towards quantitative proteomic applications. Anal Bioanal Chem 2012; 404:1057-67. [PMID: 22610548 DOI: 10.1007/s00216-012-6065-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/18/2012] [Accepted: 04/19/2012] [Indexed: 10/28/2022]
Abstract
Formaldehyde is a key fixation reagent. This review explores its application in combination with qualitative and quantitative mass spectrometry (MS). Formalin-fixed and paraffin-embedded (FFPE) tissues form a large reservoir of biologically valuable samples and their investigation by MS has only recently started. Furthermore, formaldehyde can be used to stabilise protein-protein interactions in living cells. Because formaldehyde is able to modify proteins, performing MS analysis on these samples can pose a challenge. Here we discuss the chemistry of formaldehyde cross-linking, describe the problems of and progress in these two applications and their common aspects, and evaluate the potential of these methods for the future.
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Affiliation(s)
- Cordula Klockenbusch
- The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
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Azimzadeh O, Scherthan H, Yentrapalli R, Barjaktarovic Z, Ueffing M, Conrad M, Neff F, Calzada-Wack J, Aubele M, Buske C, Atkinson MJ, Hauck SM, Tapio S. Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation. J Proteomics 2012; 75:2384-95. [DOI: 10.1016/j.jprot.2012.02.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 01/23/2023]
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Tanca A, Pagnozzi D, Addis MF. Setting proteins free: Progresses and achievements in proteomics of formalin-fixed, paraffin-embedded tissues. Proteomics Clin Appl 2011; 6:7-21. [DOI: 10.1002/prca.201100044] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/01/2011] [Accepted: 09/13/2011] [Indexed: 12/25/2022]
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Addis MF, Pisanu S, Ghisaura S, Pagnozzi D, Marogna G, Tanca A, Biosa G, Cacciotto C, Alberti A, Pittau M, Roggio T, Uzzau S. Proteomics and pathway analyses of the milk fat globule in sheep naturally infected by Mycoplasma agalactiae provide indications of the in vivo response of the mammary epithelium to bacterial infection. Infect Immun 2011; 79:3833-45. [PMID: 21690237 PMCID: PMC3165467 DOI: 10.1128/iai.00040-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 06/01/2011] [Indexed: 12/27/2022] Open
Abstract
Milk fat globules (MFGs) are vesicles released in milk as fat droplets surrounded by the endoplasmic reticulum and apical cell membranes. During formation and apocrine secretion by lactocytes, various amounts of cytoplasmic crescents remain trapped within the released vesicle, making MFGs a natural sampling mechanism of the lactating cell contents. With the aim of investigating the events occurring in the mammary epithelium during bacterial infection, the MFG proteome was characterized by two-dimensional difference gel electrophoresis (2-D DIGE), SDS-PAGE followed by shotgun liquid chromatography-tandem mass spectrometry (GeLC-MS/MS), label-free quantification by the normalized spectral abundance factor (NSAF) approach, Western blotting, and pathway analysis, using sheep naturally infected by Mycoplasma agalactiae. A number of protein classes were found to increase in MFGs upon infection, including proteins involved in inflammation and host defense, cortical cytoskeleton proteins, heat shock proteins, and proteins related to oxidative stress. Conversely, a strikingly lower abundance was observed for proteins devoted to MFG metabolism and secretion. To our knowledge, this is the first report describing proteomic changes occurring in MFGs during sheep infectious mastitis. The results presented here offer new insights into the in vivo response of mammary epithelial cells to bacterial infection and open the way to the discovery of protein biomarkers for monitoring clinical and subclinical mastitis.
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Affiliation(s)
- Maria Filippa Addis
- Porto Conte Ricerche Srl, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero SS, Italy.
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Evaluation of formalin-fixed paraffin-embedded tissues in the proteomic analysis of parathyroid glands. Proteome Sci 2011; 9:29. [PMID: 21651755 PMCID: PMC3123619 DOI: 10.1186/1477-5956-9-29] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/08/2011] [Indexed: 01/12/2023] Open
Abstract
Background Proteomic research in the field of parathyroid tissues is limited by the very small dimension of the glands and by the low incidence of cancer lesions (1%). Formalin-fixed paraffin-embedded (FFPE) tissue specimens are a potentially valuable resource for discovering protein cancer biomarkers. In this study we have verified the applicability of a heat induced protein extraction from FFPE parathyroid adenoma tissues followed by a gel-based or gel-free proteomic approach in order to achieve protein separation and identification. Results The best results for high quality MS spectra and parameters, were obtained by using a gel-free approach, and up to 163 unique proteins were identified. Similar results were obtained by applying both SDS-out and SDS-out + TCA/Acetone techniques during the gel-free method. Western blot analysis carried out with specific antibodies suggested that the antigenicity was not always preserved, while specific immunoreactions were detected for calmodulin, B box and SPRY domain-containing protein (BSPRY), peroxiredoxin 6 (PRDX 6) and parvalbumin. Conclusions In spite of some limitations mainly due to the extensive formalin-induced covalent cross-linking, our results essentially suggest the applicability of a proteomic approach to FFPE parathyroid specimens. From our point of view, FFPE extracts might be an alternative source, especially in the validation phase of protein biomarkers when a large cohort of samples is required and the low availability of frozen tissues might be constraining.
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Impact of fixation time on GeLC–MS/MS proteomic profiling of formalin-fixed, paraffin-embedded tissues. J Proteomics 2011; 74:1015-21. [DOI: 10.1016/j.jprot.2011.03.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/04/2011] [Accepted: 03/14/2011] [Indexed: 02/05/2023]
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