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Robledo-Cadena DX, Pacheco-Velazquez SC, Vargas-Navarro JL, Padilla-Flores JA, Moreno-Sanchez R, Rodríguez-Enríquez S. Mitochondrial Proteins as Metabolic Biomarkers and Sites for Therapeutic Intervention in Primary and Metastatic Cancers. Mini Rev Med Chem 2024; 24:1187-1202. [PMID: 39004839 DOI: 10.2174/0113895575254320231030051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 07/16/2024]
Abstract
Accelerated aerobic glycolysis is one of the main metabolic alterations in cancer, associated with malignancy and tumor growth. Although glycolysis is one of the most studied properties of tumor cells, recent studies demonstrate that oxidative phosphorylation (OxPhos) is the main ATP provider for the growth and development of cancer. In this last regard, the levels of mRNA and protein of OxPhos enzymes and transporters (including glutaminolysis, acetate and ketone bodies catabolism, free fatty acid β-oxidation, Krebs Cycle, respiratory chain, phosphorylating system- ATP synthase, ATP/ADP translocator, Pi carrier) are altered in tumors and cancer cells in comparison to healthy tissues and organs, and non-cancer cells. Both energy metabolism pathways are tightly regulated by transcriptional factors, oncogenes, and tumor-suppressor genes, all of which dictate their protein levels depending on the micro-environmental conditions and the type of cancer cell, favoring cancer cell adaptation and growth. In the present review paper, variation in the mRNA and protein levels as well as in the enzyme/ transporter activities of the OxPhos machinery is analyzed. An integral omics approach to mitochondrial energy metabolism pathways may allow for identifying their use as suitable, reliable biomarkers for early detection of cancer development and metastasis, and for envisioned novel, alternative therapies.
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Affiliation(s)
- Diana Xochiquetzal Robledo-Cadena
- Departamento de Bioquímica. Instituto Nacional de Cardiología. Juan Badiano No. 1. Col. Sección XVI. 14080. Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Coyoacán, México City, 04510, México
| | - Silvia Cecilia Pacheco-Velazquez
- Departamento de Bioquímica. Instituto Nacional de Cardiología. Juan Badiano No. 1. Col. Sección XVI. 14080. Ciudad de México, México
| | - Jorge Luis Vargas-Navarro
- Laboratorio de Control Metabólico. Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
| | - Joaquín Alberto Padilla-Flores
- Laboratorio de Control Metabólico. Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
| | - Rafael Moreno-Sanchez
- Laboratorio de Control Metabólico. Carrera de Biología, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
| | - Sara Rodríguez-Enríquez
- Laboratorio de Control Metabólico, Carrera de Medicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Los Reyes Ixtacala, Hab Los Reyes Ixtacala Barrio de los Árboles/Barrio de los Héroes, Tlalnepantla, 54090, México
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Mottaghi-Dastjerdi N, Ghorbani A, Montazeri H, Guzzi PH. A systems biology approach to pathogenesis of gastric cancer: gene network modeling and pathway analysis. BMC Gastroenterol 2023; 23:248. [PMID: 37482618 PMCID: PMC10364406 DOI: 10.1186/s12876-023-02891-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/18/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) ranks among the most common malignancies worldwide. This study aimed to find critical genes/pathways in GC pathogenesis. METHODS Gene interactions were analyzed, and the protein-protein interaction network was drawn. Then enrichment analysis of the hub genes was performed and network cluster analysis and promoter analysis of the hub genes were done. Age/sex analysis was done on the identified genes. RESULTS Eleven hub genes in GC were identified in the current study (ATP5A1, ATP5B, ATP5D, MT-ATP8, COX7A2, COX6C, ND4, ND6, NDUFS3, RPL8, and RPS16), mostly involved in mitochondrial functions. There was no report on the ATP5D, ND6, NDUFS3, RPL8, and RPS16 in GC. Our results showed that the most affected processes in GC are the metabolic processes, and the oxidative phosphorylation pathway was considerably enriched which showed the significance of mitochondria in GC pathogenesis. Most of the affected pathways in GC were also involved in neurodegenerative diseases. Promoter analysis showed that negative regulation of signal transduction might play an important role in GC pathogenesis. In the analysis of the basal expression pattern of the selected genes whose basal expression presented a change during the age, we found that a change in age may be an indicator of changes in disease insurgence and/or progression at different ages. CONCLUSIONS These results might open up new insights into GC pathogenesis. The identified genes might be novel diagnostic/prognostic biomarkers or potential therapeutic targets for GC. This work, being based on bioinformatics analysis act as a hypothesis generator that requires further clinical validation.
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Affiliation(s)
- Negar Mottaghi-Dastjerdi
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran.
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran.
| | - Hamed Montazeri
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Pietro Hiram Guzzi
- Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Catanzaro, Italy
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3
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Hu H, Laskin J. Emerging Computational Methods in Mass Spectrometry Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203339. [PMID: 36253139 PMCID: PMC9731724 DOI: 10.1002/advs.202203339] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/17/2022] [Indexed: 05/10/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful analytical technique that generates maps of hundreds of molecules in biological samples with high sensitivity and molecular specificity. Advanced MSI platforms with capability of high-spatial resolution and high-throughput acquisition generate vast amount of data, which necessitates the development of computational tools for MSI data analysis. In addition, computation-driven MSI experiments have recently emerged as enabling technologies for further improving the MSI capabilities with little or no hardware modification. This review provides a critical summary of computational methods and resources developed for MSI data analysis and interpretation along with computational approaches for improving throughput and molecular coverage in MSI experiments. This review is focused on the recently developed artificial intelligence methods and provides an outlook for a future paradigm shift in MSI with transformative computational methods.
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Affiliation(s)
- Hang Hu
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
| | - Julia Laskin
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
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Hou ZL, Han FY, Lou LL, Zhao WY, Huang XX, Yao GD, Song SJ. The nature compound dehydrocrenatidine exerts potent antihepatocellular carcinoma by destroying mitochondrial complexes in vitro and in vivo. Phytother Res 2022; 36:1353-1371. [PMID: 35112410 DOI: 10.1002/ptr.7398] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022]
Abstract
Cumulative evidence indicates that mitochondria dysfunction plays an important role in tumour treatment. Given the limited efficacy and toxicity of current mitochondria-targeted drugs, research into effective mitochondria-targeted anticancer agents remains an irresistible general trend. In this study, it was found that dehydrocrenatidine (DEC), a β-carbolin alkaloid isolated from Picrasma quassiodes, displays a promising growth inhibitory effect in vitro and in vivo by inducing apoptosis of hepatocellular carcinoma (HCC) cells. Mechanistically, we provided that the possible target of DEC against HCC cells was determined by isobaric labels for relative and absolute quantification assay and validated them using further experiments. The results suggested that DEC can target and regulate the function of mitochondrial complexes I, III and IV, affecting oxidative phosphorylation and ultimately leading to mitochondrial dysfunction to exert its anti-HCC effects. In addition, the combination of DEC and sorafenib showed a synergistic effect and was also associated with mitochondrial dysfunction. Importantly, DEC did not show significant toxicity in mice. This study provided a new insight into underlying mechanisms in DEC-treated HCC cells, suggesting that DEC might be a mitochondrial targeting lead compound.
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Affiliation(s)
- Zi-Lin Hou
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Feng-Ying Han
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Li-Li Lou
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Wen-Yu Zhao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
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Beuque M, Martin-Lorenzo M, Balluff B, Woodruff HC, Lucas M, de Bruin DM, van Timmeren JE, Boer OJD, Heeren RM, Meijer SL, Lambin P. Machine learning for grading and prognosis of esophageal dysplasia using mass spectrometry and histological imaging. Comput Biol Med 2021; 138:104918. [PMID: 34638018 DOI: 10.1016/j.compbiomed.2021.104918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Barrett's esophagus (BE) is a precursor lesion of esophageal adenocarcinoma and may progress from non-dysplastic through low-grade dysplasia (LGD) to high-grade dysplasia (HGD) and cancer. Grading BE is of crucial prognostic value and is currently based on the subjective evaluation of biopsies. This study aims to investigate the potential of machine learning (ML) using spatially resolved molecular data from mass spectrometry imaging (MSI) and histological data from microscopic hematoxylin and eosin (H&E)-stained imaging for computer-aided diagnosis and prognosis of BE. METHODS Biopsies from 57 patients were considered, divided into non-dysplastic (n = 15), LGD non-progressive (n = 14), LGD progressive (n = 14), and HGD (n = 14). MSI experiments were conducted at 50 × 50 μm spatial resolution per pixel corresponding to a tile size of 96x96 pixels in the co-registered H&E images, making a total of 144,823 tiles for the whole dataset. RESULTS ML models were trained to distinguish epithelial tissue from stroma with area-under-the-curve (AUC) values of 0.89 (MSI) and 0.95 (H&E)) and dysplastic grade (AUC of 0.97 (MSI) and 0.85 (H&E)) on a tile level, and low-grade progressors from non-progressors on a patient level (accuracies of 0.72 (MSI) and 0.48 (H&E)). CONCLUSIONS In summary, while the H&E-based classifier was best at distinguishing tissue types, the MSI-based model was more accurate at distinguishing dysplastic grades and patients at progression risk, which demonstrates the complementarity of both approaches. Data are available via ProteomeXchange with identifier PXD028949.
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Affiliation(s)
- Manon Beuque
- Department of Precision Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Marta Martin-Lorenzo
- Maastricht MultiModal Molecular Imaging Institute (M4I), Universiteitssingel 50, 6229 ER, Maastricht, Maastricht University, the Netherlands; Department of Immunology, IIS-Fundación Jiménez Díaz, UAM, Avda. Reyes Católicos, 28040, Madrid, Spain.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), Universiteitssingel 50, 6229 ER, Maastricht, Maastricht University, the Netherlands
| | - Henry C Woodruff
- Department of Precision Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; Department of Radiology and Nuclear Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre+, 6202 AZ, Maastricht, The Netherlands
| | - Marit Lucas
- Department of Biomedical Engineering & Physics, Amsterdam UMC, Meibergdreef 9, 1105 AZ, Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Daniel M de Bruin
- Department of Biomedical Engineering & Physics, Amsterdam UMC, Meibergdreef 9, 1105 AZ, Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Janita E van Timmeren
- Department of Precision Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; Department of Radiation Oncology, University Hospital Zurich and University of Zurich, Rämistrasse 100, 8006, Zürich, Switzerland
| | - Onno J de Boer
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Ron Ma Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4I), Universiteitssingel 50, 6229 ER, Maastricht, Maastricht University, the Netherlands
| | - Sybren L Meijer
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
| | - Philippe Lambin
- Department of Precision Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University, 6229 ER Maastricht, The Netherlands; Department of Radiology and Nuclear Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre+, 6202 AZ, Maastricht, The Netherlands
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Dong SXM, Vizeacoumar FS, Bhanumathy KK, Alli N, Gonzalez-Lopez C, Gajanayaka N, Caballero R, Ali H, Freywald A, Cassol E, Angel JB, Vizeacoumar FJ, Kumar A. Identification of novel genes involved in apoptosis of HIV-infected macrophages using unbiased genome-wide screening. BMC Infect Dis 2021; 21:655. [PMID: 34233649 PMCID: PMC8261936 DOI: 10.1186/s12879-021-06346-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/15/2021] [Indexed: 12/01/2022] Open
Abstract
Background Macrophages, besides resting latently infected CD4+ T cells, constitute the predominant stable, major non-T cell HIV reservoirs. Therefore, it is essential to eliminate both latently infected CD4+ T cells and tissue macrophages to completely eradicate HIV in patients. Until now, most of the research focus is directed towards eliminating latently infected CD4+ T cells. However, few approaches have been directed at killing of HIV-infected macrophages either in vitro or in vivo. HIV infection dysregulates the expression of many host genes essential for the survival of infected cells. We postulated that exploiting this alteration may yield novel targets for the selective killing of infected macrophages. Methods We applied a pooled shRNA-based genome-wide approach by employing a lentivirus-based library of shRNAs to screen novel gene targets whose inhibition should selectively induce apoptosis in HIV-infected macrophages. Primary human MDMs were infected with HIV-eGFP and HIV-HSA viruses. Infected MDMs were transfected with siRNAs specific for the promising genes followed by analysis of apoptosis by flow cytometry using labelled Annexin-V in HIV-infected, HIV-exposed but uninfected bystander MDMs and uninfected MDMs. The results were analyzed using student’s t-test from at least four independent experiments. Results We validated 28 top hits in two independent HIV infection models. This culminated in the identification of four target genes, Cox7a2, Znf484, Cstf2t, and Cdk2, whose loss-of-function induced apoptosis preferentially in HIV-infected macrophages. Silencing these single genes killed significantly higher number of HIV-HSA-infected MDMs compared to the HIV-HSA-exposed, uninfected bystander macrophages, indicating the specificity in the killing of HIV-infected macrophages. The mechanism governing Cox7a2-mediated apoptosis of HIV-infected macrophages revealed that targeting respiratory chain complex II and IV genes also selectively induced apoptosis of HIV-infected macrophages possibly through enhanced ROS production. Conclusions We have identified above-mentioned novel genes and specifically the respiratory chain complex II and IV genes whose silencing may cause selective elimination of HIV-infected macrophages and eventually the HIV-macrophage reservoirs. The results highlight the potential of the identified genes as targets for eliminating HIV-infected macrophages in physiological environment as part of an HIV cure strategy. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06346-7.
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Affiliation(s)
- Simon X M Dong
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kalpana K Bhanumathy
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nezeka Alli
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Niranjala Gajanayaka
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ramon Caballero
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hamza Ali
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, ON, Canada
| | - Jonathan B Angel
- Department of Medicine, the Ottawa Health Research Institute, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Franco J Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK, Canada.
| | - Ashok Kumar
- Apoptosis Research Center, Children's Hospital of Eastern Ontario, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. .,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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Jin H, Zheng W, Hou J, Peng H, Zhuo H. An Essential NRP1-Mediated Role for Tagln2 in Gastric Cancer Angiogenesis. Front Oncol 2021; 11:653246. [PMID: 34150622 PMCID: PMC8213069 DOI: 10.3389/fonc.2021.653246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/04/2021] [Indexed: 12/29/2022] Open
Abstract
Knowledge about the precise biological role and underlying mechanism of Tagln2 in tumor progression is relatively limited, especially in angiogenesis focused on tumor derived endothelial cells (ECs) has rarely been reported. Here, the function, molecular mechanism and potential clinical value of Tagln2 in gastric cancer (GC) angiogenesis were investigated. GC tissue microarrays were used to assess the expression of Tagln2 in ECs. The relationships between expression and clinicopathological features were analyzed to evaluate the clinical value of Tagln2. Gain- and loss-of-function approaches were performed in ECs to investigate the functions of Tagln2 in angiogenesis. A combination of angiogenesis antibody array, RNA-Seq analyses and a series of in vitro experiments were performed to reveal the proangiogenic mechanism mediated by NRP1. Immunohistochemistry performed on an independent tissue chip (n=75) revealed significant upregulation of Tagln2 in tumor-derived ECs which were specifically immunolabeled with CD34. Additionally, high Tagln2 levels correlated significantly with the presence of lymph node as well as distant metastases. Gain- and loss-of-function approaches highlighted the function of Tagln2 in promoting EC proliferation, motility, and capillary-like tube formation and in reducing apoptosis. Tagln2 upregulation led to significantly increased mRNA and protein levels of NRP1 and subsequently activated the NRP1/VEGFR2 and downstream MAPK signaling pathways. These data indicate the importance of Tagln2 in angiogenesis, as a potential therapeutic target, and as a candidate prognostic marker in GC.
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Affiliation(s)
- Hongwei Jin
- Xiamen Key Laboratory of Biomarker Translational Medicine, Medical Laboratory of Xiamen Humanity Hospital Fujian Medical University, Xiamen, China
| | - Wei Zheng
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, China.,Department of Gastrointestinal Surgery, Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, China
| | - Jingjing Hou
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, China.,Department of Gastrointestinal Surgery, Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, China
| | - Huifang Peng
- Department of Endocrinology, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Huiqin Zhuo
- Department of Gastrointestinal Surgery, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, China.,Department of Gastrointestinal Surgery, Xiamen Municipal Key Laboratory of Gastrointestinal Oncology, Xiamen, China
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Alteration of protein expression and spliceosome pathway activity during Barrett's carcinogenesis. J Gastroenterol 2021; 56:791-807. [PMID: 34227026 PMCID: PMC8370908 DOI: 10.1007/s00535-021-01802-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 06/18/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Barrett's esophagus (BE) is a known precursor lesion and the strongest risk factor for esophageal adenocarcinoma (EAC), a common and lethal type of cancer. Prediction of risk, the basis for efficient intervention, is commonly solely based on histologic examination. This approach is challenged by problems such as inter-observer variability in the face of the high heterogeneity of dysplastic tissue. Molecular markers might offer an additional way to understand the carcinogenesis and improve the diagnosis-and eventually treatment. In this study, we probed significant proteomic changes during dysplastic progression from BE into EAC. METHODS During endoscopic mucosa resection, epithelial and stromal tissue samples were collected by laser capture microdissection from 10 patients with normal BE and 13 patients with high-grade dysplastic/EAC. Samples were analyzed by mass spectrometry-based proteomic analysis. Expressed proteins were determined by label-free quantitation, and gene set enrichment was used to find differentially expressed pathways. The results were validated by immunohistochemistry for two selected key proteins (MSH6 and XPO5). RESULTS Comparing dysplastic/EAC to non-dysplastic BE, we found in equal volumes of epithelial tissue an overall up-regulation in terms of protein abundance and diversity, and determined a set of 226 differentially expressed proteins. Significantly higher expressions of MSH6 and XPO5 were validated orthogonally and confirmed by immunohistochemistry. CONCLUSIONS Our results demonstrate that disease-related proteomic alterations can be determined by analyzing minute amounts of cell-type-specific collected tissue. Further analysis indicated that alterations of certain pathways associated with carcinogenesis, such as micro-RNA trafficking, DNA damage repair, and spliceosome activity, exist in dysplastic/EAC.
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Mohamed SA, Taube ET, Thiele H, Noack F, Nebrich G, Mohamady K, Hanke T, Klein O. Evaluation of the Aortopathy in the Ascending Aorta: The Novelty of Using Matrix-Assisted Laser Desorption/Ionization Imaging. Proteomics Clin Appl 2021; 15:e2000047. [PMID: 33270371 DOI: 10.1002/prca.202000047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
PURPOSE Histopathological evaluation presents conflicting reports regarding aortic abnormalities. The authors aim to present proof-of-concept study to explore the feasibility of matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) in combination with histopathology for characterizing alterations in the aneurysmal ascending formalin-fixed paraffin-embedded (FFPE) aorta tissue. EXPERIMENTAL DESIGN The authors assess FFPE specimens from patients with a dilated aorta and bicuspid aortic valve (BAV), those with a standard tricuspid aortic valve (TAV), and those with Marfan syndrome (MFS) via histopathology and grade the conditions for elastic fiber fragmentation (EFF) and MALDI-IMS. The proteins using liquid chromatographic-mass spectrometry are identified and the results are confirmed by immunohistochemistry. RESULTS There is significant difference in terms of EFF between MFS and BAV, and TAV and BAV. Characteristic peptide signatures and m/z values in the EFF facilitate the characterization among the aortic specimens of BAV, MFS, and TAV. The m/z values from the aortic alpha smooth muscle actin and myosin heavy chains significantly increase in BAV compared with MFS and TAV. These findings are confirmed by immunohistochemistry. CONCLUSION The results represent a strategy that uses MALDI-IMS in combination with histopathology as promising approaches to characterize spatial alteration in the structure of the aneurysmal ascending aorta.
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Affiliation(s)
- Salah A Mohamed
- Department of Cardiac and Thoracic Vascular Surgery, UKSH-Campus Luebeck, Luebeck, 23538, Germany
| | - Eliane T Taube
- Charité-Universitaetsmedizin, Institute for Pathology, Berlin, 10117, Germany
| | - Herbert Thiele
- Fraunhofer Institute for Digital Medicine MEVIS, Luebeck, 23538, Germany
| | - Frank Noack
- Institute of Pathology Martin-Luther Hospital, Berlin, 14193, Germany
| | - Grit Nebrich
- Berlin Institute of Health Center for Regenerative Therapies & Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Campus Virchow Klinikum (CVK), Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
| | | | | | - Oliver Klein
- Berlin Institute of Health Center for Regenerative Therapies & Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Campus Virchow Klinikum (CVK), Charité - Universitätsmedizin Berlin, Berlin, 13353, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Berlin, Berlin, 13353, Germany
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Klein O, Haeckel A, Reimer U, Nebrich G, Schellenberger E. Multiplex enzyme activity imaging by MALDI-IMS of substrate library conversions. Sci Rep 2020; 10:15522. [PMID: 32968143 PMCID: PMC7511933 DOI: 10.1038/s41598-020-72436-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Enzymes are fundamental to biological processes and involved in most pathologies. Here we demonstrate the concept of simultaneously mapping multiple enzyme activities (EA) by applying enzyme substrate libraries to tissue sections and analyzing their conversion by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). To that end, we spray-applied a solution of 20 naturally derived peptides that are known substrates for proteases, kinases, and phosphatases to zinc-fixed paraffin tissue sections of mouse kidneys. After enzyme conversion for 5 to 120 min at 37 °C and matrix application, the tissue sections were imaged by MALDI-IMS. We could image incubation time-dependently 16 of the applied substrates with differing signal intensities and 12 masses of expected products. Utilizing inherent enzyme amplification, EA-IMS can become a powerful tool to locally study multiple, potentially even lowly expressed, enzyme activities, networks, and their pharmaceutical modulation. Differences in the substrate detectability highlight the need for future optimizations.
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Affiliation(s)
- Oliver Klein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Akvile Haeckel
- Department of Radiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstraße 5, 12489, Berlin, Germany
| | - Grit Nebrich
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Eyk Schellenberger
- Department of Radiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
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Heijs B, Holst-Bernal S, de Graaff MA, Briaire-de Bruijn IH, Rodriguez-Girondo M, van de Sande MAJ, Wuhrer M, McDonnell LA, Bovée JVMG. Molecular signatures of tumor progression in myxoid liposarcoma identified by N-glycan mass spectrometry imaging. J Transl Med 2020; 100:1252-1261. [PMID: 32341520 DOI: 10.1038/s41374-020-0435-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
Myxoid liposarcoma (MLS) is the second most common subtype of liposarcoma, accounting for ~6% of all sarcomas. MLS is characterized by a pathognomonic FUS-DDIT3, or rarely EWSR1-DDIT3, gene fusion. The presence of ≥5% hypercellular round cell areas is associated with a worse prognosis for the patient and is considered high grade. The prognostic significance of areas with moderately increased cellularity (intermediate) is currently unknown. Here we have applied matrix-assisted laser desorption/ionization mass spectrometry imaging to analyze the spatial distribution of N-linked glycans on an MLS microarray in order to identify molecular markers for tumor progression. Comparison of the N-glycan profiles revealed that increased relative abundances of high-mannose type glycans were associated with tumor progression. Concomitantly, an increase of the average number of mannoses on high-mannose glycans was observed. Although overall levels of complex-type glycans decreased, an increase of tri- and tetra-antennary N-glycans was observed with morphological tumor progression and increased tumor histological grade. The high abundance of tri-antennary N-glycan species was also associated with poor disease-specific survival. These findings mirror recent observations in colorectal cancer, breast cancer, ovarian cancer, and cholangiocarcinoma, and are in line with a general role of high-mannose glycans and higher-antennary complex-type glycans in cancer progression.
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Affiliation(s)
- Bram Heijs
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Stephanie Holst-Bernal
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marieke A de Graaff
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Mar Rodriguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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12
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Zhu H, Aloor A, Ma C, Kondengaden SM, Wang PG. Mass Spectrometric Analysis of Protein Glycosylation. ACS SYMPOSIUM SERIES 2020. [DOI: 10.1021/bk-2020-1346.ch010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- He Zhu
- These authors contributed equally
| | | | | | | | - Peng George Wang
- Current Address: Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, P. R. China
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Yang L, Hong Q, Xu SG, Kuang XY, Di GH, Liu GY, Wu J, Shao ZM, Yu SJ. Downregulation of transgelin 2 promotes breast cancer metastasis by activating the reactive oxygen species/nuclear factor‑κB signaling pathway. Mol Med Rep 2019; 20:4045-4258. [PMID: 31485630 PMCID: PMC6797978 DOI: 10.3892/mmr.2019.10643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 07/17/2019] [Indexed: 12/21/2022] Open
Abstract
Transgelin 2 (TAGLN2) is a cytoskeletal protein of the calponin family. Abnormal expression of TAGLN2 was observed in various types of cancer. Our previous study reported that TAGLN2 expression was reduced in lymph node-positive breast cancer patients; however, the role of TAGLN2 in breast cancer metastasis remains unknown. In the present study, the role of TAGLN2 in breast cancer metastasis was investigated in vitro and in vivo via Transwell migration, luciferase and flow cytometry assays, and a mouse xenograft model. Proteins interacting with TAGLN2 were identified via co-immunoprecipitation assays and liquid chromatography/mass spectrometry, and the signaling pathway associated with the effects of TAGLN2 was investigated. Additionally, western blotting and reverse transcription-quantitative polymerase chain reaction were performed to further explore the potential pathway in which TAGLN2 may be involved and the mechanism underlying its effects in breast cancer metastasis. The present study reported that TAGLN2 expression was increased by 11.4-fold in patients without distant metastasis compared with those positive for distant metastasis. Knockdown of TAGLN2 resulted in increased cell migration in vitro and promoted lung metastasis in vivo. Additionally, overexpression of TAGLN2 suppressed lung metastasis in a mouse model. Peroxiredoxin 1 (PRDX1), an important reactive oxygen species (ROS) regulator, was revealed to interact with TAGLN2. In addition, mitochondrial redistribution and PRDX1 downregulation were reported following TAGLN2 silencing, which promoted ROS production and nuclear factor (NF)-κB activation in breast cancer cells. This induced the expression of metastasis-associated genes, including C-X-C chemokine receptor 4, matrix metalloproteinase (MMP)1 and MMP2. The present study proposed TAGLN2 to function as a tumor suppressor and that loss of TAGLN2 may promote the metastasis of breast cancer by activating the ROS/NF-κB signaling pathway.
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Affiliation(s)
- Liu Yang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Qi Hong
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Si-Guang Xu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Xia-Ying Kuang
- Department of Breast Surgery, The First Affiliated Hospital, Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Gen-Hong Di
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Guang-Yu Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Jiong Wu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
| | - San-Jian Yu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China
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14
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Hao R, Liu Y, Du Q, Liu L, Chen S, You H, Dong Y. Transgelin-2 expression in breast cancer and its relationships with clinicopathological features and patient outcome. Breast Cancer 2019; 26:776-783. [PMID: 31144206 DOI: 10.1007/s12282-019-00981-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 11/27/2022]
Abstract
BACKGROUND Transgelin-2 is an actin-binding protein that is widely expressed in various tissues and organs of the body, and reportedly may participate in the development and progression of multiple cancers. However, the clinical significance of transgelin-2 still remains controversial. We, therefore, aimed to determine the expression of transgelin-2 in breast cancer as well as its correlation with the tumorigenesis, progression and prognosis of human breast cancer. METHODS We collected tissues of 58 breast cancer patients from our hospital and 1090 samples from The Cancer Genome Atlas (TCGA) database. X-tile software was used to divide the transgelin-2 mRNA expression level in the database, logistic regression model was used to identify independent factors influencing transgelin-2 mRNA expression, and then Cox regression and Kaplan-Meier analysis were used to find factors that influence survival of breast cancer. RESULTS Transgelin-2 was significantly overexpressed in breast cancer tissues from our hospital and receiver operating characteristic (ROC) curve indicated that transgelin-2 may have diagnostic value. Meanwhile, estrogen receptor (ER) was in inverse correlation with transgelin-2 protein and mRNA expression, and transgelin-2 expression was positively correlated with Ki67 in breast cancer tissues. Logistic regression model revealed that TNM stage, ER and progesterone receptor (PR) status were independent factors for transgelin-2 mRNA expression. Patients with high transgelin-2 mRNA expression showed a poor survival and the trend was statistically significant only in ER-negative patients. CONCLUSIONS Transgelin-2 was expressed significantly higher in breast cancer cells and correlated with some clinicopathological factors. High transgelin-2 expression might predict poor prognosis for ER-negative patients.
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Affiliation(s)
- Ruifang Hao
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yang Liu
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qian Du
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Leichao Liu
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Siying Chen
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Haisheng You
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yalin Dong
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
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15
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Cordero Hernandez Y, Boskamp T, Casadonte R, Hauberg‐Lotte L, Oetjen J, Lachmund D, Peter A, Trede D, Kriegsmann K, Kriegsmann M, Kriegsmann J, Maass P. Targeted Feature Extraction in MALDI Mass Spectrometry Imaging to Discriminate Proteomic Profiles of Breast and Ovarian Cancer. Proteomics Clin Appl 2018; 13:e1700168. [DOI: 10.1002/prca.201700168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 11/29/2018] [Indexed: 01/10/2023]
Affiliation(s)
| | - Tobias Boskamp
- Center for Industrial MathematicsUniversity of Bremen Bremen 28359 Germany
- Department for Cell BiologyUniversity of Bremen Bremen 28359 Germany
| | | | - Lena Hauberg‐Lotte
- Center for Industrial MathematicsUniversity of Bremen Bremen 28359 Germany
| | - Janina Oetjen
- Center for Industrial MathematicsUniversity of Bremen Bremen 28359 Germany
| | - Delf Lachmund
- Center for Industrial MathematicsUniversity of Bremen Bremen 28359 Germany
| | - Annette Peter
- Department for Cell BiologyUniversity of Bremen Bremen 28359 Germany
| | - Dennis Trede
- SCiLS, Bruker Daltonik GmbH Bremen 28359 Germany
| | - Katharina Kriegsmann
- Department of Hematology Oncology and RheumatologyUniversity of Heidelberg Heidelberg 69120 Germany
| | - Mark Kriegsmann
- Institute of PathologyUniversity of Heidelberg Heidelberg 69120 Germany
| | - Jörg Kriegsmann
- Proteopath GmbH Trier 54296 Germany
- Center for Histology Cytology and Molecular Diagnostic Trier 54296 Germany
| | - Peter Maass
- Center for Industrial MathematicsUniversity of Bremen Bremen 28359 Germany
- SCiLS, Bruker Daltonik GmbH Bremen 28359 Germany
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16
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Klein O, Kanter F, Kulbe H, Jank P, Denkert C, Nebrich G, Schmitt WD, Wu Z, Kunze CA, Sehouli J, Darb‐Esfahani S, Braicu I, Lellmann J, Thiele H, Taube ET. MALDI‐Imaging for Classification of Epithelial Ovarian Cancer Histotypes from a Tissue Microarray Using Machine Learning Methods. Proteomics Clin Appl 2018; 13:e1700181. [DOI: 10.1002/prca.201700181] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 10/31/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Oliver Klein
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Berlin‐Brandenburg Center for Regenerative TherapiesCharité—Universitätsmedizin Berlin 13353 Berlin Germany
| | - Frederic Kanter
- Institute of Mathematics and Image ComputingUniversität zu Lübeck Lübeck Germany
| | - Hagen Kulbe
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Department of GynecologyCharité—Universitätsmedizin Berlin 13353 Berlin Germany
- Fraunhofer—Institute for Medical Image Computing MEVIS 23562 Lübeck Germany
| | - Paul Jank
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Institute of PathologyCharité—Universitätsmedizin Berlin 10117 Berlin Germany
| | - Carsten Denkert
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Institute of PathologyCharité—Universitätsmedizin Berlin 10117 Berlin Germany
| | - Grit Nebrich
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Berlin‐Brandenburg Center for Regenerative TherapiesCharité—Universitätsmedizin Berlin 13353 Berlin Germany
| | - Wolfgang D. Schmitt
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Institute of PathologyCharité—Universitätsmedizin Berlin 10117 Berlin Germany
| | - Zhiyang Wu
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Berlin‐Brandenburg Center for Regenerative TherapiesCharité—Universitätsmedizin Berlin 13353 Berlin Germany
| | - Catarina A. Kunze
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Institute of PathologyCharité—Universitätsmedizin Berlin 10117 Berlin Germany
| | - Jalid Sehouli
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Department of GynecologyCharité—Universitätsmedizin Berlin 13353 Berlin Germany
- Fraunhofer—Institute for Medical Image Computing MEVIS 23562 Lübeck Germany
| | - Silvia Darb‐Esfahani
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Institute of Pathology Spandau 13589 Berlin Germany
| | - Ioana Braicu
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Department of GynecologyCharité—Universitätsmedizin Berlin 13353 Berlin Germany
- Fraunhofer—Institute for Medical Image Computing MEVIS 23562 Lübeck Germany
| | - Jan Lellmann
- Institute of Mathematics and Image ComputingUniversität zu Lübeck Lübeck Germany
| | - Herbert Thiele
- Fraunhofer—Institute for Medical Image Computing MEVIS 23562 Lübeck Germany
| | - Eliane T. Taube
- Charité—Universitätsmedizin Berlincorporate member of Freie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of Health Berlin Germany
- Institute of PathologyCharité—Universitätsmedizin Berlin 10117 Berlin Germany
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Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
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Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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18
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Mascini NE, Teunissen J, Noorlag R, Willems SM, Heeren RM. Tumor classification with MALDI-MSI data of tissue microarrays: A case study. Methods 2018; 151:21-27. [DOI: 10.1016/j.ymeth.2018.04.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/04/2018] [Accepted: 04/09/2018] [Indexed: 11/25/2022] Open
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19
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Klein O, Strohschein K, Nebrich G, Fuchs M, Thiele H, Giavalisco P, Duda GN, Winkler T, Kobarg JH, Trede D, Geissler S. Unraveling local tissue changes within severely injured skeletal muscles in response to MSC-based intervention using MALDI Imaging mass spectrometry. Sci Rep 2018; 8:12677. [PMID: 30140012 PMCID: PMC6107672 DOI: 10.1038/s41598-018-30990-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Pre-clinical and clinical studies are now beginning to demonstrate the high potential of cell therapies in enhancing muscle regeneration. We previously demonstrated functional benefit after the transplantation of autologous bone marrow mesenchymal stromal cells (MSC-TX) into a severe muscle crush trauma model. Despite our increasing understanding of the molecular and cellular mechanisms underlying MSC's regenerative function, little is known about the local molecular alterations and their spatial distribution within the tissue after MSC-TX. Here, we used MALDI imaging mass spectrometry (MALDI-IMS) in combination with multivariate statistical strategies to uncover previously unknown peptide alterations within severely injured skeletal muscles. Our analysis revealed that very early molecular alterations in response to MSC-TX occur largely in the region adjacent to the trauma and only to a small extent in the actual trauma region. Using "bottom up" mass spectrometry, we subsequently identified the proteins corresponding to the differentially expressed peptide intensity distributions in the specific muscle regions and used immunohistochemistry to validate our results. These findings extend our current understanding about the early molecular processes of muscle healing and highlights the critical role of trauma adjacent tissue during the early therapeutic response upon treatment with MSC.
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Affiliation(s)
- Oliver Klein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - Kristin Strohschein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Grit Nebrich
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Michael Fuchs
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Herbert Thiele
- Fraunhofer - Inst. Medical Image Computing MEVIS, Maria-Goeppert-Straße 3, 23562, Lübeck, Germany
| | - Patrick Giavalisco
- Experimental Systems Biology Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg, 14476, Golm, Germany
| | - Georg N Duda
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Tobias Winkler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jan Hendrik Kobarg
- SCiLS, Zweigniederlassung Bremen der Bruker Daltonik, Fahrenheitstr. 1, 28359, Bremen, Germany
| | - Dennis Trede
- SCiLS, Zweigniederlassung Bremen der Bruker Daltonik, Fahrenheitstr. 1, 28359, Bremen, Germany
| | - Sven Geissler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Julius Wolff Institute & Center for Musculoskeletal Surgery, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
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20
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Sun Y, Peng W, He W, Luo M, Chang G, Shen J, Zhao X, Hu Y. Transgelin-2 is a novel target of KRAS-ERK signaling involved in the development of pancreatic cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:166. [PMID: 30041673 PMCID: PMC6056937 DOI: 10.1186/s13046-018-0818-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/29/2018] [Indexed: 02/08/2023]
Abstract
Background The KRAS mutation is the driving force of pancreatic ductal adenocarcinoma (PDAC). Downstream effectors of KRAS signal pathways are crucial to the development of PDAC. The purpose of this study was to investigate the relationship between KRAS mutation and transgelin-2. Transgelin-2 is highly expressed in PDAC tissues compared with adjacent normal tissues. The underlying mechanism for upregulating transgelin-2 is largely unknown. Methods Expression of transgelin-2 was analyzed by microarray data and qRT-PCR. The effect of KRAS signaling on transgelin-2 expression was examined in PDAC cells in the presence or absence of the ERK inhibitor. The interaction of transgelin-2 with ERK was confirmed by immunoprecipitation. ERK-mediated Phosphorylation of transglein-2 was detected by in vivo and in vitro kinase assays. The gain-of-function and loss-of-function approaches were used to examine the role of phosphorylation of transgelin-2 on cell proliferation. Phosphorylation of transgelin-2 was detected by immunohistochemistry in PDAC tissues. Results Here we found transgelin-2 expression was induced by KRAS mutation. In the case of KRAS mutation, ERK2 interacted with 29–31 amino acids of transgelin-2 and subsequently phosphorylated the S145 residue of transgelin-2. S145 phosphorylation of transgelin-2 played important roles in cell proliferation and tumorigenesis of PDAC. In addition, S145 phosphorylation of transgelin-2 was associated with a poor prognosis in patients with PDAC. Conclusions This study indicated that KRAS-ERK-mediated transeglin-2 phosphorylation played an important role in the development of PDAC. Inhibition of transgelin-2 phosphorylation may be a potential therapeutic strategy for targeting PDAC with KRAS mutation.
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Affiliation(s)
- Yan Sun
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Wenfang Peng
- Department of Endocrinology, Shanghai Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200336, China
| | - Weiwei He
- Department of Thoracic Surgery, Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200233, China
| | - Man Luo
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Guilin Chang
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jiping Shen
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaoping Zhao
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Yu Hu
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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Klein O, Hanke T, Nebrich G, Yan J, Schubert B, Giavalisco P, Noack F, Thiele H, Mohamed SA. Imaging Mass Spectrometry for Characterization of Atrial Fibrillation Subtypes. Proteomics Clin Appl 2018; 12:e1700155. [DOI: 10.1002/prca.201700155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/24/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Oliver Klein
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and; Berlin Institute of Health Berlin-Brandenburg Center for Regenerative Therapies; 13353 Berlin Germany
| | - Thorsten Hanke
- Department of Cardiac and Thoracic Vascular Surgery; University of Luebeck; 23538 Luebeck Germany
| | - Grit Nebrich
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and; Berlin Institute of Health Berlin-Brandenburg Center for Regenerative Therapies; 13353 Berlin Germany
| | - Junfeng Yan
- Department of Cardiac and Thoracic Vascular Surgery; University of Luebeck; 23538 Luebeck Germany
| | - Benedikt Schubert
- Department of Cardiac and Thoracic Vascular Surgery; University of Luebeck; 23538 Luebeck Germany
| | - Patrick Giavalisco
- Experimental Systems Biology; Max Planck Institute of Molecular Plant Physiology; 14476 Golm Germany
| | - Frank Noack
- Institute of Pathology; Martin-Luther Hospital; 14193 Berlin Germany
| | - Herbert Thiele
- Fraunhofer Institute for Medical Image Computing MEVIS; 23538 Luebeck Germany
| | - Salah A. Mohamed
- Department of Cardiac and Thoracic Vascular Surgery; University of Luebeck; 23538 Luebeck Germany
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22
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Lin L, Zheng J, Yu Q, Chen W, Xing J, Chen C, Tian R. High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis. J Proteomics 2017; 174:9-16. [PMID: 29278786 DOI: 10.1016/j.jprot.2017.12.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/28/2017] [Accepted: 12/19/2017] [Indexed: 12/18/2022]
Abstract
Mass spectrometry (MS)-based serum proteome analysis is extremely challenging due to its high complexity and dynamic range of protein abundances. Developing high throughput and accurate serum proteomic profiling approach capable of analyzing large cohorts is urgently needed for biomarker discovery. Herein, we report a streamlined workflow for fast and accurate proteomic profiling from 1μL of blood serum. The workflow combined an integrated technique for highly sensitive and reproducible sample preparation and a new data-independent acquisition (DIA)-based MS method. Comparing with standard data dependent acquisition (DDA) approach, the optimized DIA method doubled the number of detected peptides and proteins with better reproducibility. Without protein immunodepletion and prefractionation, the single-run DIA analysis enables quantitative profiling of over 300 proteins with 50min gradient time. The quantified proteins span more than five orders of magnitude of abundance range and contain over 50 FDA-approved disease markers. The workflow allowed us to analyze 20 serum samples per day, with about 358 protein groups per sample being identified. A proof-of-concept study on renal cell carcinoma (RCC) serum samples confirmed the feasibility of the workflow for large scale serum proteomic profiling and disease-related biomarker discovery. BIOLOGICAL SIGNIFICANCE Blood serum or plasma is the predominant specimen for clinical proteomic studies while the analysis is extremely challenging for its high complexity. Many efforts had been made in the past for serum proteomics for maximizing protein identifications, whereas few have been concerned with throughput and reproducibility. Here, we establish a rapid, robust and high reproducible DIA-based workflow for streamlined serum proteomic profiling from 1μL serum. The workflow doesn't need protein depletion and pre-fractionation, while still being able to detect disease-relevant proteins accurately. The workflow is promising in clinical application, because the usage of small sample amounts makes blood testing much less invasive, the fully integrated sample preparation by the SISPROT technology greatly improve sample preparation throughput and reproducibility, and the scan feature of DIA method provides a way to convert nonrenewable clinical specimens into permanent digital proteome maps which could be easily reanalyzed.
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Affiliation(s)
- Lin Lin
- Materials Characterization & Preparation Center, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Jiaxin Zheng
- Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Quan Yu
- Division of Advanced Manufacturing, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Wendong Chen
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jinchun Xing
- Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Chenxi Chen
- Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Ruijun Tian
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
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23
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Guran R, Vanickova L, Horak V, Krizkova S, Michalek P, Heger Z, Zitka O, Adam V. MALDI MSI of MeLiM melanoma: Searching for differences in protein profiles. PLoS One 2017; 12:e0189305. [PMID: 29220390 PMCID: PMC5722329 DOI: 10.1371/journal.pone.0189305] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/23/2017] [Indexed: 12/21/2022] Open
Abstract
Background Treatment of advanced cutaneous melanoma remains challenging, and new data on melanoma biology are required. The most widely accepted criteria for the prognostic evaluation of melanoma are histopathological and clinical parameters, and the identification of additional tumor markers is thus of paramount importance. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI), an important tool in cancer research, is useful for unraveling the molecular profile of melanoma. Methodology/Principal findings In this report, we used the melanoma-bearing Libechov minipig (MeLiM), a unique animal model that allows observation of the complete spontaneous regression of invasive cutaneous melanoma, to investigate i) the differences between melanoma and healthy skin protein profiles and ii) the proteins potentially involved in spontaneous regression. The MeLiM tissues were cryosected, histologically characterized, analyzed by MALDI MSI, and immunohistologically stained. Multivariate statistical analyses of the MALDI MSI data revealed ten relevant m/z ions, of which the expression levels varied significantly among the studied MeLiM tissues. These ion peaks were used to create mass ion images/maps and visualize the differences between tumor and healthy skin specimens, as well as among histologically characterized tissue regions. Conclusions/Significance Protein profiles comprising ten statistically significant mass ion peaks useful for differentiating cutaneous melanoma and healthy skin tissues were determined. Peaks at m/z 3044, 6011, 6140 and 10180 were overexpressed in melanoma compared with healthy skin tissue. More specifically, m/z 6140 was expressed at significantly (p < 0.05) higher levels in normally growing melanoma regions than in regions with early and late spontaneous regression. This study demonstrates the clinical utility of MALDI MSI for the analysis of tissue cryosections at a molecular level.
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Affiliation(s)
- Roman Guran
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Lucie Vanickova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
| | - Vratislav Horak
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Libechov, Czech Republic
| | - Sona Krizkova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Petr Michalek
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, Czech Republic
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
- * E-mail:
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24
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Matrix-Assisted Laser Desorption/Ionisation Mass Spectrometry Imaging in the Study of Gastric Cancer: A Mini Review. Int J Mol Sci 2017; 18:ijms18122588. [PMID: 29194417 PMCID: PMC5751191 DOI: 10.3390/ijms18122588] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide and the disease outcome commonly depends upon the tumour stage at the time of diagnosis. However, this cancer can often be asymptomatic during the early stages and remain undetected until the later stages of tumour development, having a significant impact on patient prognosis. However, our comprehension of the mechanisms underlying the development of gastric malignancies is still lacking. For these reasons, the search for new diagnostic and prognostic markers for gastric cancer is an ongoing pursuit. Modern mass spectrometry imaging (MSI) techniques, in particular matrix-assisted laser desorption/ionisation (MALDI), have emerged as a plausible tool in clinical pathology as a whole. More specifically, MALDI-MSI is being increasingly employed in the study of gastric cancer and has already elucidated some important disease checkpoints that may help us to better understand the molecular mechanisms underpinning this aggressive cancer. Here we report the state of the art of MALDI-MSI approaches, ranging from sample preparation to statistical analysis, and provide a complete review of the key findings that have been reported in the literature thus far.
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25
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Deng S, Li Y, Yi G, Lei B, Guo M, Xiang W, Chen Z, Liu Y, Qi S. Overexpression of COX7A2 is associated with a good prognosis in patients with glioma. J Neurooncol 2017; 136:41-50. [PMID: 29079956 DOI: 10.1007/s11060-017-2637-z] [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] [Received: 07/12/2017] [Accepted: 10/14/2017] [Indexed: 12/15/2022]
Abstract
Cytochrome c oxidase subunit 7A2 (COX7A2) is a nuclear-encoded polypeptide involved in assembly and regulation of cytochrome c oxidase (COX). Changes in the respiratory chain as big complex are known to be associated with cancer, but little research has been performed to discover COX7A2 as a prognostic marker in glioma. In the present study, we investigated COX7A2 expression and its prognostic significance in glioma. Glioma surgical tissue samples were taken from 126 patients who had been followed up from 4 to 51 months. Immunohistochemistry were used to test COX7A2 expression in the 126 tumor samples. Eighty-six of 126 (68.3%) paraffin-embedded glioma biopsies showed high expression of COX7A2. Statistical analysis displayed that there was significant difference of COX7A2 expression level in patients categorized according to WHO classification. Kaplan-Meier survival analysis revealed that patients with higher COX7A2 expression had longer overall survival time and better prognosis. R2: microarray analysis based on Tumor Glioma French 284 database, Tumor Glioblastoma TCGA 540 database, and Tumor Glioma Kawaguchi 50 database testified that high expression of COX7A2 is associated with a good prognosis in patients with glioma. Multivariate analysis showed that COX7A2 high expression was an independent prognostic indicator for survival. Our results suggest that COX7A2 could be served as a valuable prognostic marker of glioma.
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Affiliation(s)
- Shengze Deng
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838#, Guangzhou, 510515, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yaomin Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838#, Guangzhou, 510515, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Guozhong Yi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838#, Guangzhou, 510515, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Bingxi Lei
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838#, Guangzhou, 510515, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Manlan Guo
- Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Wei Xiang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838#, Guangzhou, 510515, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Ziyang Chen
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838#, Guangzhou, 510515, Guangdong, China.,Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yawei Liu
- Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou Dadao Bei Street 1838#, Guangzhou, 510515, Guangdong, China. .,Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
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26
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Lou S, Balluff B, de Graaff MA, Cleven AHG, Briaire-de Bruijn I, Bovée JVMG, McDonnell LA. High-grade sarcoma diagnosis and prognosis: Biomarker discovery by mass spectrometry imaging. Proteomics 2017; 16:1802-13. [PMID: 27174013 DOI: 10.1002/pmic.201500514] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 12/24/2022]
Abstract
The combination of high heterogeneity, both intratumoral and intertumoral, with their rarity has made diagnosis, prognosis of high-grade sarcomas difficult. There is an urgent need for more objective molecular biomarkers, to differentiate between the many different subtypes, and to also provide new treatment targets. Mass spectrometry imaging (MSI) has amply demonstrated its ability to identify potential new markers for patient diagnosis, survival, metastasis and response to therapy in cancer research. In this study, we investigated the ability of MALDI-MSI of proteins to distinguish between high-grade osteosarcoma (OS), leiomyosarcoma (LMS), myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) (Ntotal = 53). We also investigated if there are individual proteins or protein signatures that are statistically associated with patient survival. Twenty diagnostic protein signals were found characteristic for specific tumors (p ≤ 0.05), amongst them acyl-CoA-binding protein (m/z 11 162), macrophage migration inhibitory factor (m/z 12 350), thioredoxin (m/z 11 608) and galectin-1 (m/z 14 633) were assigned. Another nine protein signals were found to be associated with overall survival (p ≤ 0.05), including proteasome activator complex subunit 1 (m/z 9753), indicative for non-OS patients with poor survival; and two histone H4 variants (m/z 11 314 and 11 355), indicative of poor survival for LMS patients.
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Affiliation(s)
- Sha Lou
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Balluff
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, The Netherlands
| | - Marieke A de Graaff
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | - Arjen H G Cleven
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | | | - Judith V M G Bovée
- Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands
| | - Liam A McDonnell
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Leiden University, Medical Center, Leiden, The Netherlands.,Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
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27
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Kiso K, Yoshifuji H, Oku T, Hikida M, Kitagori K, Hirayama Y, Nakajima T, Haga H, Tsuruyama T, Miyagawa-Hayashino A. Transgelin-2 is upregulated on activated B-cells and expressed in hyperplastic follicles in lupus erythematosus patients. PLoS One 2017; 12:e0184738. [PMID: 28910360 PMCID: PMC5599031 DOI: 10.1371/journal.pone.0184738] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/30/2017] [Indexed: 01/23/2023] Open
Abstract
Transgelin-2 (TAGLN2) is an actin-binding protein that controls actin stability and promotes T cell activation. TAGLN2 is also expressed on B-cells but its function in B-cells is unknown. We found that TAGLN2-expressing B-cells were localized in the germinal center (GC) of secondary lymphoid tissues and TAGLN2 mRNA was significantly upregulated after IgM+IgG stimulation in primary human B-cells, suggesting that TAGLN2 was upregulated upon B-cell activation. In support of this, lymph nodes (LNs) from patients with systemic lupus erythematosus (SLE), in which the intense GC activity have been recognized, showed increased TAGLN2 expression in B-cells compared to control LNs. Moreover, TAGLN2+B-cells were distributed widely not only in the GC but also in the perifollicular areas in SLE LNs. In contrast, CD19+ B-cells and CD19+CD27+ memory-B cells in peripheral blood of SLE patients showed no increase in TAGLN2 mRNA. Two-photon excitation microscopy of Raji cells demonstrated that TAGLN2 colocalized with F-actin and moved together to the periphery upon stimulation. TAGLN2-knockdown in Raji cells resulted in impaired phosphorylation of PLCγ2 leading to inhibition of cell migration. Microarray analysis of TAGLN2-knockdown Raji cells showed decreased expression of the genes associated with immune function including CCR6 and as well as of those associated with regulation of the actin cytoskeleton including ABI2, compared to controls. These results suggest that TAGLN2 might regulate activation and migration of B-cells, in particular, the entry of activated B-cells into the follicle. We also suggest that TAGLN2 could be used as a marker for activated B-cells.
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Affiliation(s)
- Kaori Kiso
- Center for Anatomical, Pathological and Forensic Medical Research, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuma Oku
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Portfolio & Science, Drug Discovery Research, Astellas Pharma Inc, Tsukuba, Japan
| | - Masaki Hikida
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Laboratory for Molecular Cell Physiology, Department of Life Science, Akita University
| | - Koji Kitagori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitaka Hirayama
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Portfolio & Science, Drug Discovery Research, Astellas Pharma Inc, Tsukuba, Japan
| | - Toshiki Nakajima
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Tatsuaki Tsuruyama
- Center for Anatomical, Pathological and Forensic Medical Research, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aya Miyagawa-Hayashino
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
- * E-mail:
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28
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O'Neill JR, Pak HS, Pairo-Castineira E, Save V, Paterson-Brown S, Nenutil R, Vojtěšek B, Overton I, Scherl A, Hupp TR. Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins. Mol Cell Proteomics 2017; 16:1138-1150. [PMID: 28336725 PMCID: PMC5461543 DOI: 10.1074/mcp.m116.065078] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/26/2017] [Indexed: 12/11/2022] Open
Abstract
Esophageal cancer is the eighth most common cancer worldwide and the majority of patients have systemic disease at presentation. Esophageal adenocarcinoma (OAC), the predominant subtype in western countries, is largely resistant to current chemotherapy regimens. Selective markers are needed to enhance clinical staging and to allow targeted therapies yet there are minimal proteomic data on this cancer type. After histological review, lysates from OAC and matched normal esophageal and gastric samples from seven patients were subjected to LC MS/MS after tandem mass tag labeling and OFFGEL fractionation. Patient matched samples of OAC, normal esophagus, normal stomach, lymph node metastases and uninvolved lymph nodes were used from an additional 115 patients for verification of expression by immunohistochemistry (IHC). Over six thousand proteins were identified and quantified across samples. Quantitative reproducibility was excellent between technical replicates and a moderate correlation was seen across samples with the same histology. The quantitative accuracy was verified across the dynamic range for seven proteins by immunohistochemistry (IHC) on the originating tissues. Multiple novel tumor-specific candidates are proposed and EPCAM was verified by IHC. This shotgun proteomic study of OAC used a comparative quantitative approach to reveal proteins highly expressed in specific tissue types. Novel tumor-specific proteins are proposed and EPCAM was demonstrated to be specifically overexpressed in primary tumors and lymph node metastases compared with surrounding normal tissues. This candidate and others proposed in this study could be developed as tumor-specific targets for novel clinical staging and therapeutic approaches.
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Affiliation(s)
- J Robert O'Neill
- From the ‡Edinburgh Cancer Research Centre at the Institute of Genetics and Molecular Medicine, Edinburgh University; Robert.o'.,§Department of Surgery, Royal Infirmary of Edinburgh
| | - Hui-Song Pak
- ¶Department of Human Protein Sciences, Faculty of Medicine, University of Geneva
| | - Erola Pairo-Castineira
- ‖Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh.,**MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh University
| | - Vicki Save
- ‡‡Department of Pathology, Royal Infirmary of Edinburgh
| | | | - Rudolf Nenutil
- §§Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno
| | - Bořivoj Vojtěšek
- §§Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno
| | - Ian Overton
- ‖Centre for Medical Informatics, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh.,**MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh University
| | - Alex Scherl
- ¶Department of Human Protein Sciences, Faculty of Medicine, University of Geneva
| | - Ted R Hupp
- From the ‡Edinburgh Cancer Research Centre at the Institute of Genetics and Molecular Medicine, Edinburgh University.,§§Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno
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29
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Casadonte R, Longuespée R, Kriegsmann J, Kriegsmann M. MALDI IMS and Cancer Tissue Microarrays. Adv Cancer Res 2017; 134:173-200. [PMID: 28110650 DOI: 10.1016/bs.acr.2016.11.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) technology creates a link between the molecular assessment of numerous molecules and the morphological information about their special distribution. The application of MALDI IMS on formalin-fixed paraffin-embedded (FFPE) tissue microarrays (TMAs) is suitable for large-scale discovery analyses. Data acquired from FFPE TMA cancer samples in current research are very promising, and applications for routine diagnostics are under development. With the current rapid advances in both technology and applications, MALDI IMS technology is expected to enter into routine diagnostics soon. This chapter is intended to be comprehensive with respect to all aspects and considerations for the application of MALDI IMS on FFPE cancer TMAs with in-depth notes on technical aspects.
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Affiliation(s)
| | | | - J Kriegsmann
- Proteopath GmbH, Trier, Germany; Institute of Molecular Pathology, Trier, Germany; Center for Histology, Cytology and Molecular Diagnostics, Trier, Germany
| | - M Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany.
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30
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Arentz G, Mittal P, Zhang C, Ho YY, Briggs M, Winderbaum L, Hoffmann MK, Hoffmann P. Applications of Mass Spectrometry Imaging to Cancer. Adv Cancer Res 2017; 134:27-66. [PMID: 28110654 DOI: 10.1016/bs.acr.2016.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pathologists play an essential role in the diagnosis and prognosis of benign and cancerous tumors. Clinicians provide tissue samples, for example, from a biopsy, which are then processed and thin sections are placed onto glass slides, followed by staining of the tissue with visible dyes. Upon processing and microscopic examination, a pathology report is provided, which relies on the pathologist's interpretation of the phenotypical presentation of the tissue. Targeted analysis of single proteins provide further insight and together with clinical data these results influence clinical decision making. Recent developments in mass spectrometry facilitate the collection of molecular information about such tissue specimens. These relatively new techniques generate label-free mass spectra across tissue sections providing nonbiased, nontargeted molecular information. At each pixel with spatial coordinates (x/y) a mass spectrum is acquired. The acquired mass spectrums can be visualized as intensity maps displaying the distribution of single m/z values of interest. Based on the sample preparation, proteins, peptides, lipids, small molecules, or glycans can be analyzed. The generated intensity maps/images allow new insights into tumor tissues. The technique has the ability to detect and characterize tumor cells and their environment in a spatial context and combined with histological staining, can be used to aid pathologists and clinicians in the diagnosis and management of cancer. Moreover, such data may help classify patients to aid therapy decisions and predict outcomes. The novel complementary mass spectrometry-based methods described in this chapter will contribute to the transformation of pathology services around the world.
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Affiliation(s)
- G Arentz
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Mittal
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - C Zhang
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - Y-Y Ho
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M Briggs
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia; ARC Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, SA, Australia
| | - L Winderbaum
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - M K Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia
| | - P Hoffmann
- Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide, SA, Australia.
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31
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Abstract
One of the big clinical challenges in the treatment of cancer is the different behavior of cancer patients under guideline therapy. An important determinant for this phenomenon has been identified as inter- and intratumor heterogeneity. While intertumor heterogeneity refers to the differences in cancer characteristics between patients, intratumor heterogeneity refers to the clonal and nongenetic molecular diversity within a patient. The deciphering of intratumor heterogeneity is recognized as key to the development of novel therapeutics or treatment regimens. The investigation of intratumor heterogeneity is challenging since it requires an untargeted molecular analysis technique that accounts for the spatial and temporal dynamics of the tumor. So far, next-generation sequencing has contributed most to the understanding of clonal evolution within a cancer patient. However, it falls short in accounting for the spatial dimension. Mass spectrometry imaging (MSI) is a powerful tool for the untargeted but spatially resolved molecular analysis of biological tissues such as solid tumors. As it provides multidimensional datasets by the parallel acquisition of hundreds of mass channels, multivariate data analysis methods can be applied for the automated annotation of tissues. Moreover, it integrates the histology of the sample, which enables studying the molecular information in a histopathological context. This chapter will illustrate how MSI in combination with statistical methods and histology has been used for the description and discovery of intratumor heterogeneity in different cancers. This will give evidence that MSI constitutes a unique tool for the investigation of intratumor heterogeneity, and could hence become a key technology in cancer research.
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Abstract
Over the last decade mass spectrometry imaging (MSI) has been integrated in to many areas of drug discovery and development. It can have significant impact in oncology drug discovery as it allows efficacy and safety of compounds to be assessed against the backdrop of the complex tumour microenvironment. We will discuss the roles of MSI in investigating compound and metabolite biodistribution and defining pharmacokinetic -pharmacodynamic relationships, analysis that is applicable to all drug discovery projects. We will then look more specifically at how MSI can be used to understand tumour metabolism and other applications specific to oncology research. This will all be described alongside the challenges of applying MSI to industry research with increased use of metrology for MSI.
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Huang KT, Ludy S, Calligaris D, Dunn IF, Laws E, Santagata S, Agar NYR. Rapid Mass Spectrometry Imaging to Assess the Biochemical Profile of Pituitary Tissue for Potential Intraoperative Usage. Adv Cancer Res 2016; 134:257-282. [PMID: 28110653 DOI: 10.1016/bs.acr.2016.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pituitary adenomas are relatively common intracranial neoplasms that are frequently treated with surgical resection. Rapid visualization of pituitary tissue remains a challenge as current techniques either produce little to no information on hormone-secreting function or are too slow to practically aid in intraoperative or even perioperative decision-making. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) represents a powerful method by which molecular maps of tissue samples can be created, yielding a two-dimensional representation of the expression patterns of small molecules and proteins from biologic samples. In this chapter, we review the use of MALDI MSI, its application to the characterization of the pituitary gland, and its potential applications for guiding the management of pituitary adenomas.
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Affiliation(s)
- K T Huang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - S Ludy
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - D Calligaris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - I F Dunn
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - E Laws
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - S Santagata
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - N Y R Agar
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.
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Kriegsmann M, Longuespée R, Wandernoth P, Mohanu C, Lisenko K, Weichert W, Warth A, Dienemann H, De Pauw E, Katzenberger T, Aust D, Baretton G, Kriegsmann J, Casadonte R. Typing of colon and lung adenocarcinoma by high throughput imaging mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:858-864. [PMID: 27939606 DOI: 10.1016/j.bbapap.2016.11.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
Abstract
In advanced tumor stages, diagnosis is frequently made from metastatic tumor tissue. In some cases, the identification of the tumor of origin may be difficult by histology alone. In this setting, immunohistochemical and molecular biological methods are often required. In a subset of tumors definite diagnosis cannot be achieved. Thus, additional new diagnostic methods are required for precise tumor subtyping. Mass spectrometric methods are of special interest for the discrimination of different tumor types. We investigated whether it is possible to discern adenocarcinomas of colon and lung using high-throughput imaging mass spectrometry on formalin-fixed paraffin-embedded tissue microarrays. 101 primary adenocarcinoma of the colon and 91 primary adenocarcinoma of the lung were used to train a Linear Discriminant Analysis model. Results were validated on an independent set of 116 colonic and 75 lung adenocarcinomas. In the validation cohort 109 of 116 patients with colonic and 67 of 75 patients with lung adenocarcinomas were correctly classified. The ability to define proteomic profiles capable to discern different tumor types promises a valuable tool in cancer diagnostics and might complement current approaches. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
| | | | | | | | - Katharina Lisenko
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
| | | | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Germany.
| | - Hendrik Dienemann
- Department of Thoracic Surgery, Thoraxklinik at Heidelberg University, Heidelberg, Germany.
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Belgium.
| | | | - Daniela Aust
- Institute of Pathology, University Hospital Carl Gustav Carus, Dresden, Germany.
| | - Gustavo Baretton
- Institute of Pathology, University Hospital Carl Gustav Carus, Dresden, Germany.
| | - Joerg Kriegsmann
- Proteopath GmbH, Trier, Germany; Center for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany.
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Boskamp T, Lachmund D, Oetjen J, Cordero Hernandez Y, Trede D, Maass P, Casadonte R, Kriegsmann J, Warth A, Dienemann H, Weichert W, Kriegsmann M. A new classification method for MALDI imaging mass spectrometry data acquired on formalin-fixed paraffin-embedded tissue samples. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:916-926. [PMID: 27836618 DOI: 10.1016/j.bbapap.2016.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/28/2022]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) shows a high potential for applications in histopathological diagnosis, and in particular for supporting tumor typing and subtyping. The development of such applications requires the extraction of spectral fingerprints that are relevant for the given tissue and the identification of biomarkers associated with these spectral patterns. We propose a novel data analysis method based on the extraction of characteristic spectral patterns (CSPs) that allow automated generation of classification models for spectral data. Formalin-fixed paraffin embedded (FFPE) tissue samples from N=445 patients assembled on 12 tissue microarrays were analyzed. The method was applied to discriminate primary lung and pancreatic cancer, as well as adenocarcinoma and squamous cell carcinoma of the lung. A classification accuracy of 100% and 82.8%, resp., could be achieved on core level, assessed by cross-validation. The method outperformed the more conventional classification method based on the extraction of individual m/z values in the first application, while achieving a comparable accuracy in the second. LC-MS/MS peptide identification demonstrated that the spectral features present in selected CSPs correspond to peptides relevant for the respective classification. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Tobias Boskamp
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany; SCiLS GmbH, Bremen, Germany.
| | - Delf Lachmund
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany
| | - Janina Oetjen
- MALDI Imaging Lab, University of Bremen, Bremen, Germany
| | | | | | - Peter Maass
- Center for Industrial Mathematics, University of Bremen, Bremen, Germany; MALDI Imaging Lab, University of Bremen, Bremen, Germany; SCiLS GmbH, Bremen, Germany
| | | | - Jörg Kriegsmann
- Proteopath GmbH, Trier, Germany; Center for Histology, Cytology and Molecular Diagnostic, Trier, Germany
| | - Arne Warth
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hendrik Dienemann
- Thoraxklinik Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
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Schwamborn K, Kriegsmann M, Weichert W. MALDI imaging mass spectrometry - From bench to bedside. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:776-783. [PMID: 27810414 DOI: 10.1016/j.bbapap.2016.10.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/24/2016] [Accepted: 10/28/2016] [Indexed: 10/20/2022]
Abstract
Today, pathologists face many challenges in defining the precise morphomolecular diagnosis and in guiding clinicians to the optimal patients' treatment. To achieve this goal, increasingly, classical histomorphological methods have to be supplemented by high throughput molecular assays. Since MALDI imaging mass spectrometry (IMS) enables the assessment of spatial molecular arrangements in tissue sections, it goes far beyond microscopy in providing hundreds of different molecular images from a single scan without the need of target-specific reagents. Thus, this technology has the potential to uncover new markers for diagnostic purposes or markers that correlate with disease severity as well as prognosis and therapeutic response. Additionally, in the future MALDI IMS based classifiers measured with this technology in real time in the diagnostic setting might be applicable in the routine diagnostic setting. In this review, recently published studies that show the usefulness, advantages, and applicability of MALDI IMS in different fields of pathology (diagnosis, prognosis and treatment response) are highlighted. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Kristina Schwamborn
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany.
| | - Mark Kriegsmann
- University of Heidelberg, Department of Pathology, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München (TUM), Munich, Germany
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Abstract
INTRODUCTION Esophageal cancer (EC) is one of the most common causes of cancer-related death worldwide. Identifying suitable biomarkers for early diagnosis as well as predicting lymph node metastasis, prognosis and the therapeutic response of EC is essential for the effective and efficient management for EC. There is an urgent need to develop effective, novel approaches for patients who do not respond to conventional treatment. Areas covered: EC is characterized by the presence of two main histological types such as squamous cell carcinoma and adenocarcinoma, which differ in their response to treatments and prognosis. Thus, this review describes the latest research into biomarkers and novel treatment targets generated by cancer proteomics for the two main histological types. Finally, the main difficulties facing the translation of biomarkers and novel treatment targets into the clinical settings are discussed. Expert commentary: EC proteomics have provided useful results and, after their validation, novel clinical tools should be developed to improve the clinical outcomes for EC patients.
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Affiliation(s)
- Norihisa Uemura
- a Department of Gastroenterological Surgery , Aichi Cancer Center Hospital , Nagoya , Japan
| | - Tadashi Kondo
- b Division of Rare Cancer Research, Department of Innovative Seeds Evaluation , National Cancer Center Research Institute , Tokyo , Japan
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An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments. Anal Bioanal Chem 2016; 408:6729-40. [DOI: 10.1007/s00216-016-9793-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/01/2016] [Accepted: 07/12/2016] [Indexed: 12/29/2022]
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Ly A, Buck A, Balluff B, Sun N, Gorzolka K, Feuchtinger A, Janssen KP, Kuppen PJK, van de Velde CJH, Weirich G, Erlmeier F, Langer R, Aubele M, Zitzelsberger H, McDonnell L, Aichler M, Walch A. High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue. Nat Protoc 2016; 11:1428-43. [PMID: 27414759 DOI: 10.1038/nprot.2016.081] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue specimens are the gold standard for histological examination, and they provide valuable molecular information in tissue-based research. Metabolite assessment from archived tissue samples has not been extensively conducted because of a lack of appropriate protocols and concerns about changes in metabolite content or chemical state due to tissue processing. We present a protocol for the in situ analysis of metabolite content from FFPE samples using a high-mass-resolution matrix-assisted laser desorption/ionization fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR-MSI) platform. The method involves FFPE tissue sections that undergo deparaffinization and matrix coating by 9-aminoacridine before MALDI-MSI. Using this platform, we previously detected ∼1,500 m/z species in the mass range m/z 50-1,000 in FFPE samples; the overlap compared with fresh frozen samples is 72% of m/z species, indicating that metabolites are largely conserved in FFPE tissue samples. This protocol can be reproducibly performed on FFPE tissues, including small samples such as tissue microarrays and biopsies. The procedure can be completed in a day, depending on the size of the sample measured and raster size used. Advantages of this approach include easy sample handling, reproducibility, high throughput and the ability to demonstrate molecular spatial distributions in situ. The data acquired with this protocol can be used in research and clinical practice.
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Affiliation(s)
- Alice Ly
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Karin Gorzolka
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Gregor Weirich
- Institute of Pathology, Technische Universität München, Munich, Germany
| | | | - Rupert Langer
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Michaela Aubele
- Institute of Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Liam McDonnell
- Centre for Proteomics and Metabolomics, Leiden University Medical Centre, Leiden, the Netherlands.,Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
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Longuespée R, Casadonte R, Kriegsmann M, Pottier C, Picard de Muller G, Delvenne P, Kriegsmann J, De Pauw E. MALDI mass spectrometry imaging: A cutting-edge tool for fundamental and clinical histopathology. Proteomics Clin Appl 2016; 10:701-19. [PMID: 27188927 DOI: 10.1002/prca.201500140] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/07/2016] [Accepted: 05/13/2016] [Indexed: 01/16/2023]
Abstract
Histopathological diagnoses have been done in the last century based on hematoxylin and eosin staining. These methods were complemented by histochemistry, electron microscopy, immunohistochemistry (IHC), and molecular techniques. Mass spectrometry (MS) methods allow the thorough examination of various biocompounds in extracts and tissue sections. Today, mass spectrometry imaging (MSI), and especially matrix-assisted laser desorption ionization (MALDI) imaging links classical histology and molecular analyses. Direct mapping is a major advantage of the combination of molecular profiling and imaging. MSI can be considered as a cutting edge approach for molecular detection of proteins, peptides, carbohydrates, lipids, and small molecules in tissues. This review covers the detection of various biomolecules in histopathological sections by MSI. Proteomic methods will be introduced into clinical histopathology within the next few years.
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Affiliation(s)
- Rémi Longuespée
- Proteopath GmbH, Trier, Germany.,Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | | | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | | | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Jörg Kriegsmann
- Proteopath GmbH, Trier, Germany.,MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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Lokman NA, Pyragius CE, Ruszkiewicz A, Oehler MK, Ricciardelli C. Annexin A2 and S100A10 are independent predictors of serous ovarian cancer outcome. Transl Res 2016; 171:83-95.e1-2. [PMID: 26925708 DOI: 10.1016/j.trsl.2016.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/20/2016] [Accepted: 02/02/2016] [Indexed: 11/28/2022]
Abstract
Annexin A2, a calcium phospholipid binding protein, has been shown to play an important role in ovarian cancer metastasis. This study examined whether annexin A2 and S100A10 can be used as prognostic markers in serous ovarian cancer. ANXA2 and S100A10 gene expressions were assessed in publicly available ovarian cancer data sets and annexin A2 and S100A10 protein expressions were assessed by immunohistochemistry in a uniform cohort of stage III serous ovarian cancers (n = 109). Kaplan-Meier and Cox regression analyses were performed to assess the relationship between annexin A2 or S100A10 messenger RNA (mRNA) and protein expressions with clinical outcome. High ANXA2 mRNA levels in stage III serous ovarian cancers were associated with reduced progression-free survival (PFS; P = 0.023) and overall survival (OS; P = 0.0038), whereas high S100A10 mRNA levels predicted reduced OS (P = 0.0019). Using The Cancer Genome Atlas data sets, ANXA2 but not S100A10 expression was associated with higher clinical stage (P = 0.005), whereas both ANXA2 and S100A10 expressions were associated with the mesenchymal molecular subtype (P < 0.0001). Kaplan-Meier and Cox regression analyses showed that high stromal annexin A2 immunostaining was significantly associated with reduced PFS (P = 0.013) and OS (P = 0.044). Moreover, high cytoplasmic S100A10 staining was significantly associated with reduced OS (P = 0.027). Multivariate Cox regression analysis showed stromal annexin A2 (P = 0.009) and cytoplasmic S100A10 (P = 0.016) levels to be independent predictors of OS. Patients with high stromal annexin A2 and high cytoplasmic S100A10 expressions had a 3.4-fold increased risk of progression (P = 0.02) and 7.9-fold risk of ovarian cancer death (P = 0.04). Our findings indicate that together annexin A2 and S100A10 expressions are powerful predictors of serous ovarian cancer outcome.
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Affiliation(s)
- Noor A Lokman
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia; Adelaide Proteomics Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Carmen E Pyragius
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew Ruszkiewicz
- Centre of Cancer Biology, University of South Australia, Adelaide, South Australia, Australia; Department of Anatomical Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Martin K Oehler
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia; Department of Gynaecological Oncology, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Carmela Ricciardelli
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia.
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Lahiri S, Sun N, Buck A, Imhof A, Walch A. MALDI imaging mass spectrometry as a novel tool for detecting histone modifications in clinical tissue samples. Expert Rev Proteomics 2016; 13:275-84. [DOI: 10.1586/14789450.2016.1146598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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43
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Du YY, Zhao LM, Chen L, Sang MX, Li J, Ma M, Liu JF. The tumor-suppressive function of miR-1 by targeting LASP1 and TAGLN2 in esophageal squamous cell carcinoma. J Gastroenterol Hepatol 2016; 31:384-93. [PMID: 26414725 DOI: 10.1111/jgh.13180] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 08/06/2015] [Accepted: 08/26/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVE This study determined the expression of microRNA-1 in esophageal squamous cell carcinoma (ESCC) tissue and cell lines to evaluate its effects on clinicopathological parameters and its target genes LASP1 and TAGLN2. METHODS The expression of miR-1, lasp1, and tagln2 was detected in 55 ESCC tissues and adjacent normal tissues by reverse transcription-polymerase chain reaction (RT-PCR). The association between miR-1, lasp1, and tagln2 expression and clinicopathological characteristics was observed. MicroRNA-1 (mimics-miR-1) and its inhibitor (Inhibitor-miR-1) were transfected into esophageal cancer cells KYSE 510 and Eca 109; cell proliferation, migration, and invasion assays were carried out. Plasmid construction and dual-luciferase reporter assay were also carried out to indicate whether LASP1 and TAGLN2 were miR-1 target genes. The expression of LASP1 and TAGLN2 was detected with Western blot methods in cell lines, by immunohistochemistry in ESCC tissue. RESULTS The gene expression level of microRNA-1 in cancer tissues was significantly lower than that in adjacent normal tissues (P < 0.01). The expression of miR-1 in ESCC was correlated with involvement of lymph nodes (P = 0.002), histologic classification (P = 0.000), and vessel invasion (P = 0.022). The expression of lasp1 and tagln2 increased in cancer tissues compared with in adjacent normal tissues (P < 0.05). MiR-1 suppresses the cell growth, migration, and invasion in vitro. The expression of LASP1 and TAGLN2 decreased in mimics-miR-1 transfected cells, and increased in inhibitor-miR-1 transfected cells. Luciferase reporter assay confirmed that LASP1 and TAGLN2 mRNA actually had the target sites of miR-1. CONCLUSIONS miR-1 suppresses cell proliferation, invasiveness, metastasis, and progression of ESCC by binding its targeted genes LASP1 and TAGLN2.
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Affiliation(s)
- Yan-Yan Du
- Department of Clinical Laboratory, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Lian-Mei Zhao
- Scientific Research Center, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Liang Chen
- Scientific Research Center, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Mei-Xiang Sang
- Scientific Research Center, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Jie Li
- Scientific Research Center, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Ming Ma
- Scientific Research Center, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
| | - Jun-Feng Liu
- Department of Thoracic Surgery, Fourth Hospital, Hebei Medical University, Shijiazhuang, China
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44
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Coghlin C, Murray GI. Progress in the development of protein biomarkers of oesophageal and gastric cancers. Proteomics Clin Appl 2016; 10:532-45. [DOI: 10.1002/prca.201500079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/10/2015] [Accepted: 11/12/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Caroline Coghlin
- Department of Cellular Pathology; Craigavon Area Hospital; Portadown UK
| | - Graeme I. Murray
- Pathology, Division of Applied Medicine, School of Medicine and Dentistry; University of Aberdeen; Aberdeen UK
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Wang X, Han J, Hardie DB, Yang J, Borchers CH. The use of matrix coating assisted by an electric field (MCAEF) to enhance mass spectrometric imaging of human prostate cancer biomarkers. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:86-95. [PMID: 26757076 DOI: 10.1002/jms.3728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
In this work, we combined a newly developed matrix coating technique - matrix coating assisted by an electric field (MCAEF) and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to enhance the imaging of peptides and proteins in tissue specimens of human prostate cancer. MCAEF increased the signal-to-noise ratios of the detected proteins by a factor of 2 to 5, and 232 signals were detected within the m/z 3500-37500 mass range on a time-of-flight mass spectrometer and with the sinapinic acid MALDI matrix. Among these species, three proteins (S100-A9, S100-A10, and S100-A12) were only observed in the cancerous cell region and 14 proteins, including a fragment of mitogen-activated protein kinase/extracellular signal-regulated kinase kinase kinase 2, a fragment of cAMP-regulated phosphoprotein 19, 3 apolipoproteins (C-I, A-I, and A-II), 2 S100 proteins (A6 and A8), β-microseminoprotein, tumor protein D52, α-1-acid glycoprotein 1, heat shock protein β-1, prostate-specific antigen, and 2 unidentified large peptides at m/z 5002.2 and 6704.2, showed significantly differential distributions at the p < 0.05 (t-test) level between the cancerous and the noncancerous regions of the tissue. Among these 17 species, the distributions of apolipoprotein C-I, S100-A6, and S100-A8 were verified by immunohistological staining. In summary, this study resulted in the imaging of the largest group of proteins in prostate cancer tissues by MALDI-MS reported thus far, and is the first to show a correlation between S100 proteins and prostate cancer in a MS imaging study. The successful imaging of the three proteins only found in the cancerous tissues, as well as those showing differential expressions demonstrated the potential of MCAEF-MALDI/MS for the in situ detection of potential cancer biomarkers. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xiaodong Wang
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, #3101-4464 Markham St., Vancouver Island Technology Park, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC, V8P 5C2, Canada
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Jin H, Cheng X, Pei Y, Fu J, Lyu Z, Peng H, Yao Q, Jiang Y, Luo L, Zhuo H. Identification and verification of transgelin-2 as a potential biomarker of tumor-derived lung-cancer endothelial cells by comparative proteomics. J Proteomics 2015; 136:77-88. [PMID: 26721444 DOI: 10.1016/j.jprot.2015.12.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED To investigate heterogeneity of endothelial cells (ECs) in the tumor microenvironment and biomarkers for antitumor angiogenesis therapy, high-purity (>98%) normal (NECs) and tumor-derived CD105(+) ECs (TECs) were purified from a mouse Lewis lung carcinoma model bearing 0.5 cm tumors by immunomagnetic separation. Proteomics analysis revealed that 48 proteins (28 upregulated and 20 downregulated) were differentially regulated by at least 1.5-fold in TECs, and that these proteins were involved in metabolism, energy pathways, protein folding, cell growth and/or functioned as structural constituents of the cytoskeleton. Upregulation of heat shock protein 60 (Hspd1) and transgelin-2 (Tagln2) was revealed in TECs, and by immunohistochemistry (IHC) in paired tissues from 30 consecutive lung cancer (LC) patients. Higher expression levels of Hspd1, Tagln2 were detected in microvascular ECs of paratumor and tumor tissues than in paired normal counterparts. Stronger Tagln2 staining was associated with clinical stage, tumor size, and histological neural invasion. Higher Hspd1 (area under the curve [AUC], 0.82) and lower Tagln2 (AUC, 0.90) levels were detected in LC patient sera. Pearson correlation analysis revealed a positive correlation between serum Hspd1 and Tagln2 levels. In conclusion, higher Tagln2 levels were associated with tumor development, lymph node metastasis, and neural invasion in LC and may thus serve as a potential biomarker of tumor angiogenesis. SIGNIFICANCE High-purity endothelial cells (normal and tumor derived) were prepared to characterize ECs heterogeneity in the tumor microenvironment and to explore biomarkers of early stages of tumor development by proteomics. Candidate proteins Hspd1 and Tagln2, were further verification in the sera and tumor tissues of lung cancer patients. Moreover, higher Tagln2 was significantly associated with clinical tumor development, metastasis, and neural invasion. All these results indicated a crucial role for Tagln2 in TECs for tumor development and metastasis.
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Affiliation(s)
- Hongwei Jin
- Xiamen Center of Clinical Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Xiao Cheng
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Yihua Pei
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Jianguo Fu
- Hospital Infection Control Office, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Zhi Lyu
- Respiratory Department, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Huifang Peng
- State Key Laboratory of Stress Cell Biology, School of Life Science, Xiamen University, Xiamen, Fujian 361004, China
| | - Qin Yao
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China
| | - Yu Jiang
- Central Laboratory, Xiamen Women's and Children's Hospital, Xiamen, Fujian 361004, China.
| | - Lianzhong Luo
- Department of Pharmacy, Xiamen Medical College, Xiamen, Fujian 361004, China.
| | - Huiqin Zhuo
- Central Laboratory, The Affiliated Zhongshan Hospital, Xiamen University, Xiamen, Fujian 361004, China.
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MALDI mass spectrometry imaging analysis of pituitary adenomas for near-real-time tumor delineation. Proc Natl Acad Sci U S A 2015. [PMID: 26216958 DOI: 10.1073/pnas.1423101112] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We present a proof of concept study designed to support the clinical development of mass spectrometry imaging (MSI) for the detection of pituitary tumors during surgery. We analyzed by matrix-assisted laser desorption/ionization (MALDI) MSI six nonpathological (NP) human pituitary glands and 45 hormone secreting and nonsecreting (NS) human pituitary adenomas. We show that the distribution of pituitary hormones such as prolactin (PRL), growth hormone (GH), adrenocorticotropic hormone (ACTH), and thyroid stimulating hormone (TSH) in both normal and tumor tissues can be assessed by using this approach. The presence of most of the pituitary hormones was confirmed by using MS/MS and pseudo-MS/MS methods, and subtyping of pituitary adenomas was performed by using principal component analysis (PCA) and support vector machine (SVM). Our proof of concept study demonstrates that MALDI MSI could be used to directly detect excessive hormonal production from functional pituitary adenomas and generally classify pituitary adenomas by using statistical and machine learning analyses. The tissue characterization can be completed in fewer than 30 min and could therefore be applied for the near-real-time detection and delineation of pituitary tumors for intraoperative surgical decision-making.
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48
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Addie RD, Balluff B, Bovée JVMG, Morreau H, McDonnell LA. Current State and Future Challenges of Mass Spectrometry Imaging for Clinical Research. Anal Chem 2015; 87:6426-33. [DOI: 10.1021/acs.analchem.5b00416] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ruben D. Addie
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Balluff
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Liam A. McDonnell
- Center for Proteomics
and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
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49
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Jang SH, Jun CD, Park ZY. Label-free quantitative phosphorylation analysis of human transgelin2 in Jurkat T cells reveals distinct phosphorylation patterns under PKA and PKC activation conditions. Proteome Sci 2015; 13:14. [PMID: 25844069 PMCID: PMC4384351 DOI: 10.1186/s12953-015-0070-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 02/27/2015] [Indexed: 12/31/2022] Open
Abstract
Background Transgelin2, one of cytoskeletal actin binding proteins has recently been suggested to be involved in the formation of immune synapses. Although detailed function of transgelin2 is largely unknown, interactions between transgelin2 and actin appear to be important in regulating cellular functions of transgelin2. Because protein phosphorylation can change ability to interact with other proteins, comprehensive phosphorylation analysis of transgelin2 will be helpful in understanding its functional mechanisms. Results Here, a specific protein label-free quantitative phosphorylation analysis method combining immuno-precipitation, IMAC phosphopeptide enrichment technique and label-free relative quantification analysis was used to monitor the phosphorylation changes of transgelin2 overexpressed in Jurkat T cells under protein kinase C (PKC) and protein kinase A (PKA) activation conditions, two representative intracellular signalling pathways of immune cell activation and homeostasis. A total of six serine/threonine phosphorylation sites were identified including threonine-84, a novel phosphorylation site. Notably, distinct phosphorylation patterns of transgelin2 under the two kinase activation conditions were observed. Most phosphorylation sites showing specific kinase-dependent phosphorylation changes were discretely located in two previously characterized actin-binding regions: actin-binding site (ABS) and calponin repeat domain (CNR). PKC activation increased phosphorylation of threonine-180 and serine-185 in the CNR, and PKA activation increased phosphorylation of serine-163 in the ABS. Conclusions Multiple actin-binding regions of transgelin2 participate to accomplish its full actin-binding capability, and the actin-binding affinity of each actin-binding region appears to be modulated by specific kinase-dependent phosphorylation changes. Accordingly, different actin-binding properties or cellular functions of transgelin2 may result from distinct intracellular signalling events under immune response activation or homeostasis conditions. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0070-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Se Hwan Jang
- School of Life Sciences, Gwangju Institute of Science & Technology, 123, Cheomdangwagi-Ro, Buk-Gu, 500-712 Gwangju Republic of Korea
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science & Technology, 123, Cheomdangwagi-Ro, Buk-Gu, 500-712 Gwangju Republic of Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science & Technology, 123, Cheomdangwagi-Ro, Buk-Gu, 500-712 Gwangju Republic of Korea
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50
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Boellner S, Becker KF. Reverse Phase Protein Arrays-Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use. MICROARRAYS 2015; 4:98-114. [PMID: 27600215 PMCID: PMC4996393 DOI: 10.3390/microarrays4020098] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/19/2022]
Abstract
Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed.
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Affiliation(s)
- Stefanie Boellner
- Institut für Pathologie, Technische Universität München, Trogerstrasse 18, 81675 München, Germany.
| | - Karl-Friedrich Becker
- Institut für Pathologie, Technische Universität München, Trogerstrasse 18, 81675 München, Germany.
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