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Bernardo RA, de Oliveira Júnior CI, Roque JV, Costa NDL, Roriz VM, Sorgi CA, Janfelt C, Vaz BG, Chaves AR. Oral Squamous Cell Carcinoma Lipid Evaluation in Gingiva Tissue Stored in TRIzol via Shotgun Lipidomics and MALDI Mass Spectrometry Imaging. J Proteome Res 2024; 23:2750-2761. [PMID: 37830917 DOI: 10.1021/acs.jproteome.3c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is the prevalent type of oral cavity cancer, requiring precise, accurate, and affordable diagnosis to identify the disease in early stages, Comprehending the differences in lipid profiles between healthy and cancerous tissues encompasses great relevance in identifying biomarker candidates and enhancing the odds of successful cancer treatment. Therefore, the present study evaluates the analytical performance of simultaneous mRNA and lipid extraction in gingiva tissue from healthy patients and patients diagnosed with OSCC preserved in TRIzol reagent. The data was analyzed by partial least-squares discriminant analysis (PLS-DA) and confirmed via matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). The lipid extraction in TRIzol solution was linear in a range from 330 to 2000 ng mL-1, r2 > 0.99, intra and interday precision and accuracy <15%, and absolute recovery values ranging from 90 to 110%. The most important lipids for tumor classification were evaluated by MALDI-MSI, revealing that the lipids responsible for distinguishing the OSCC group are more prevalent in the cancerous tissue in contrast to the healthy group. The results exhibit the possibilities to do transcriptomic and lipidomic analyses in the same sample and point out important candidates related to the presence of OSCC.
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Affiliation(s)
| | - Charles Ivo de Oliveira Júnior
- Instituto de Química, Universidade Federal de Goiás, 74690-900 Goiânia, Goiás, Brazil
- Departamento de Química, Universidade Federal de Jataí, 75801-615 Jataí, Goiás, Brazil
| | - Jussara Valente Roque
- Instituto de Química, Universidade Federal de Goiás, 74690-900 Goiânia, Goiás, Brazil
| | - Nádia do Lago Costa
- Faculdade de Odontologia, Universidade Federal de Goiás, 74605-020 Goiânia, Goiás, Brazil
| | - Virgílio Moreira Roriz
- Faculdade de Odontologia, Universidade Federal de Goiás, 74605-020 Goiânia, Goiás, Brazil
| | - Carlos Arterio Sorgi
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14015-130 Ribeirão Preto, São Paulo, Brazil
| | - Christian Janfelt
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Boniek Gontijo Vaz
- Instituto de Química, Universidade Federal de Goiás, 74690-900 Goiânia, Goiás, Brazil
| | - Andréa Rodrigues Chaves
- Instituto de Química, Universidade Federal de Goiás, 74690-900 Goiânia, Goiás, Brazil
- Departamento de Química, Universidade Federal de Jataí, 75801-615 Jataí, Goiás, Brazil
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2
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Bitto V, Hönscheid P, Besso MJ, Sperling C, Kurth I, Baumann M, Brors B. Enhancing mass spectrometry imaging accessibility using convolutional autoencoders for deriving hypoxia-associated peptides from tumors. NPJ Syst Biol Appl 2024; 10:57. [PMID: 38802379 PMCID: PMC11130291 DOI: 10.1038/s41540-024-00385-x] [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: 01/12/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Mass spectrometry imaging (MSI) allows to study cancer's intratumoral heterogeneity through spatially-resolved peptides, metabolites and lipids. Yet, in biomedical research MSI is rarely used for biomarker discovery. Besides its high dimensionality and multicollinearity, mass spectrometry (MS) technologies typically output mass-to-charge ratio values but not the biochemical compounds of interest. Our framework makes particularly low-abundant signals in MSI more accessible. We utilized convolutional autoencoders to aggregate features associated with tumor hypoxia, a parameter with significant spatial heterogeneity, in cancer xenograft models. We highlight that MSI captures these low-abundant signals and that autoencoders can preserve them in their latent space. The relevance of individual hyperparameters is demonstrated through ablation experiments, and the contribution from original features to latent features is unraveled. Complementing MSI with tandem MS from the same tumor model, multiple hypoxia-associated peptide candidates were derived. Compared to random forests alone, our autoencoder approach yielded more biologically relevant insights for biomarker discovery.
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Affiliation(s)
- Verena Bitto
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- HIDSS4Health - Helmholtz Information and Data Science School for Health, Karlsruhe/Heidelberg, Heidelberg, Germany.
- Faculty for Mathematics and Computer Science, Heidelberg University, Heidelberg, Germany.
| | - Pia Hönscheid
- National Center for Tumor Diseases (NCT), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Hospital Carl Gustav Carus (UKD), Technische Universität Dresden, Institute of Pathology, Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - María José Besso
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Sperling
- National Center for Tumor Diseases (NCT), Partner Site Dresden, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Hospital Carl Gustav Carus (UKD), Technische Universität Dresden, Institute of Pathology, Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ina Kurth
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
| | - Michael Baumann
- Division of Radiooncology/Radiobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Medical Faculty Heidelberg and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
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3
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Zhao H, Shi C, Han W, Luo G, Huang Y, Fu Y, Lu W, Hu Q, Shang Z, Yang X. Advanced progress of spatial metabolomics in head and neck cancer research. Neoplasia 2024; 47:100958. [PMID: 38142528 PMCID: PMC10788507 DOI: 10.1016/j.neo.2023.100958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/15/2023] [Indexed: 12/26/2023]
Abstract
Head and neck cancer ranks as the sixth most prevalent malignancy, constituting 5 % of all cancer cases. Its inconspicuous onset often leads to advanced stage diagnoses, prompting the need for early detection to enhance patient prognosis. Currently, research into early diagnostic markers relies predominantly on genomics, proteomics, transcriptomics, and other methods, which, unfortunately, necessitate tumor tissue homogenization, resulting in the loss of temporal and spatial information. Emerging as a recent addition to the omics toolkit, spatial metabolomics stands out. This method conducts in situ mass spectrometry analyses on fresh tissue specimens while effectively preserving their spatiotemporal information. The utilization of spatial metabolomics in life science research offers distinct advantages. This article comprehensively reviews the progress of spatial metabolomics in head and neck cancer research, encompassing insights into cancer cell metabolic reprogramming. Various mass spectrometry imaging techniques, such as secondary ion mass spectrometry, stroma-assisted laser desorption/ionization, and desorption electrospray ionization, enable in situ metabolite analysis for head and neck cancer. Finally, significant emphasis is placed on the application of presently available techniques for early diagnosis, margin assessment, and prognosis of head and neck cancer.
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Affiliation(s)
- Huiting Zhao
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University. Zhenjiang 212001, China; School of Stomatology, Jinzhou Medical University, Jinzhou 121001, China
| | - Chaowen Shi
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wei Han
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | - Guanfa Luo
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University. Zhenjiang 212001, China
| | - Yumeng Huang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University. Zhenjiang 212001, China
| | - Yujuan Fu
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University. Zhenjiang 212001, China; School of Stomatology, Jinzhou Medical University, Jinzhou 121001, China
| | - Wen Lu
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University. Zhenjiang 212001, China
| | - Qingang Hu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | | | - Xihu Yang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Jiangsu University. Zhenjiang 212001, China; School of Stomatology, Jinzhou Medical University, Jinzhou 121001, China.
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4
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Uras I, Karayel-Basar M, Sahin B, Baykal AT. Detection of early proteomic alterations in 5xFAD Alzheimer's disease neonatal mouse model via MALDI-MSI. Alzheimers Dement 2023; 19:4572-4589. [PMID: 36934297 DOI: 10.1002/alz.13008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 03/20/2023]
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative disorder, characterized by memory deficit and dementia. AD is considered a multifactorial disorder where multiple processes like amyloid-beta and tau accumulation, axonal degeneration, synaptic plasticity, and autophagic processes plays an important role. In this study, the spatial proteomic differences in the neonatal 5xFAD brain tissue were investigated using MALDI-MSI coupled to LC-MS/MS, and the statistically significantly altered proteins were associated with AD. Thirty-five differentially expressed proteins (DEPs) between the brain tissues of neonatal 5xFAD and their littermate mice were detected via MALDI-MSI technique. Among the 35 proteins identified, 26 of them were directly associated with AD. Our results indicated a remarkable resemblance in the protein expression profiles of neonatal 5xFAD brain when compared to AD patient specimens or AD mouse models. These findings showed that the molecular alterations in the AD brain existed even at birth and that some proteins are neurodegenerative presages in neonatal AD brain. HIGHLIGHTS: Spatial proteomic alterations in the 5xFAD mouse brain compared to the littermate. 26 out of 35 differentially expressed proteins associated with Alzheimer's disease (AD). Molecular alterations and neurodegenerative presages in neonatal AD brain. Alterations in the synaptic function an early and common neurobiological thread.
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Affiliation(s)
- Irep Uras
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Merve Karayel-Basar
- Department of Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed Clinical Laboratories, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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5
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Iravani S, Conrad TOF. An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:151-161. [PMID: 35007196 DOI: 10.1109/tcbb.2022.3141656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Analyzing mass spectrometry-based proteomics data with deep learning (DL) approaches poses several challenges due to the high dimensionality, low sample size, and high level of noise. Additionally, DL-based workflows are often hindered to be integrated into medical settings due to the lack of interpretable explanation. We present DLearnMS, a DL biomarker detection framework, to address these challenges on proteomics instances of liquid chromatography-mass spectrometry (LC-MS) - a well-established tool for quantifying complex protein mixtures. Our DLearnMS framework learns the clinical state of LC-MS data instances using convolutional neural networks. Based on the trained neural networks, we show how biomarkers can be identified using layer-wise relevance propagation. This enables detecting discriminating regions of the data and the design of more robust networks. One of the main advantages over other established methods is that no explicit preprocessing step is needed in our DLearnMS framework. Our evaluation shows that DLearnMS outperforms conventional LC-MS biomarker detection approaches in identifying fewer false positive peaks while maintaining a comparable amount of true positives peaks. Code availability: The code is available from the following GIT repository: https://github.com/SaharIravani/DlearnMS.
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6
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Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022; 10:proteomes10040035. [PMID: 36278695 PMCID: PMC9590004 DOI: 10.3390/proteomes10040035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Immunohistochemistry (IHC) is still widely used as a morphology-based assay for in situ analysis of target proteins as specific tumor antigens. However, as a very heterogeneous collection of neoplastic diseases, breast cancer (BC) requires an accurate identification and characterization of larger panels of candidate biomarkers, beyond ER, PR, and HER2 proteins, for diagnosis and personalized treatment, without the limited availability of antibodies that are required to identify specific proteins. Top-down, middle-down, and bottom-up mass spectrometry (MS)-based proteomics approaches complement traditional histopathological tissue analysis to examine expression, modification, and interaction of hundreds to thousands of proteins simultaneously. In this review, we discuss the proteomics-based identification of dysregulated proteins in BC that are essential for the following issues: discovery and validation of new biomarkers by analysis of solid and liquid/non-invasive biopsies, cell lines, organoids and xenograft models; identification of panels of biomarkers for early detection and accurate discrimination between cancer, benign and normal tissues; identification of subtype-specific and stage-specific protein expression profiles in BC grading and measurement of disease progression; characterization of new subtypes of BC; characterization and quantitation of post-translational modifications (PTMs) and aberrant protein-protein interactions (PPI) involved in tumor development; characterization of the global remodeling of BC tissue homeostasis, diagnosis and prognostic information; and deciphering of molecular functions, biological processes and mechanisms through which the dysregulated proteins cause tumor initiation, invasion, and treatment resistance.
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7
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Pertzborn D, Arolt C, Ernst G, Lechtenfeld OJ, Kaesler J, Pelzel D, Guntinas-Lichius O, von Eggeling F, Hoffmann F. Multi-Class Cancer Subtyping in Salivary Gland Carcinomas with MALDI Imaging and Deep Learning. Cancers (Basel) 2022; 14:4342. [PMID: 36077876 PMCID: PMC9454426 DOI: 10.3390/cancers14174342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
Salivary gland carcinomas (SGC) are a heterogeneous group of tumors. The prognosis varies strongly according to its type, and even the distinction between benign and malign tumor is challenging. Adenoid cystic carcinoma (AdCy) is one subgroup of SGCs that is prone to late metastasis. This makes accurate tumor subtyping an important task. Matrix-assisted laser desorption/ionization (MALDI) imaging is a label-free technique capable of providing spatially resolved information about the abundance of biomolecules according to their mass-to-charge ratio. We analyzed tissue micro arrays (TMAs) of 25 patients (including six different SGC subtypes and a healthy control group of six patients) with high mass resolution MALDI imaging using a 12-Tesla magnetic resonance mass spectrometer. The high mass resolution allowed us to accurately detect single masses, with strong contributions to each class prediction. To address the added complexity created by the high mass resolution and multiple classes, we propose a deep-learning model. We showed that our deep-learning model provides a per-class classification accuracy of greater than 80% with little preprocessing. Based on this classification, we employed methods of explainable artificial intelligence (AI) to gain further insights into the spectrometric features of AdCys.
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Affiliation(s)
- David Pertzborn
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Christoph Arolt
- Institute of Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany
| | - Günther Ernst
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Oliver J. Lechtenfeld
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany
- ProVIS−Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany
| | - Jan Kaesler
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany
| | - Daniela Pelzel
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Orlando Guntinas-Lichius
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Ferdinand von Eggeling
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
| | - Franziska Hoffmann
- Innovative Biophotonics & MALDI Imaging, ENT Department, Jena University Hospital, 07747 Jena, Germany
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8
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Katsaounou K, Nicolaou E, Vogazianos P, Brown C, Stavrou M, Teloni S, Hatzis P, Agapiou A, Fragkou E, Tsiaoussis G, Potamitis G, Zaravinos A, Andreou C, Antoniades A, Shiammas C, Apidianakis Y. Colon Cancer: From Epidemiology to Prevention. Metabolites 2022; 12:metabo12060499. [PMID: 35736432 PMCID: PMC9229931 DOI: 10.3390/metabo12060499] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/01/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers affecting humans, with a complex genetic and environmental aetiology. Unlike cancers with known environmental, heritable, or sex-linked causes, sporadic CRC is hard to foresee and has no molecular biomarkers of risk in clinical use. One in twenty CRC cases presents with an established heritable component. The remaining cases are sporadic and associated with partially obscure genetic, epigenetic, regenerative, microbiological, dietary, and lifestyle factors. To tackle this complexity, we should improve the practice of colonoscopy, which is recommended uniformly beyond a certain age, to include an assessment of biomarkers indicative of individual CRC risk. Ideally, such biomarkers will be causal to the disease and potentially modifiable upon dietary or therapeutic interventions. Multi-omics analysis, including transcriptional, epigenetic as well as metagenomic, and metabolomic profiles, are urgently required to provide data for risk analyses. The aim of this article is to provide a perspective on the multifactorial derailment of homeostasis leading to the initiation of CRC, which may be explored via multi-omics and Gut-on-Chip analysis to identify much-needed predictive biomarkers.
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Affiliation(s)
- Kyriaki Katsaounou
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (K.K.); (S.T.)
| | | | - Paris Vogazianos
- Stremble Ventures Ltd., Limassol 4042, Cyprus; (P.V.); (C.B.); (A.A.)
| | - Cameron Brown
- Stremble Ventures Ltd., Limassol 4042, Cyprus; (P.V.); (C.B.); (A.A.)
| | - Marios Stavrou
- Department of Electrical and Computer Engineering, University of Cyprus, Nicosia 2109, Cyprus; (M.S.); (C.A.)
| | - Savvas Teloni
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (K.K.); (S.T.)
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Vari 16672, Greece;
| | - Agapios Agapiou
- Department of Chemistry, University of Cyprus, Nicosia 2109, Cyprus;
| | | | | | | | - Apostolos Zaravinos
- Department of Life Sciences, European University Cyprus, Nicosia 1516, Cyprus;
- Basic and Translational Cancer Research Center, Nicosia 1516, Cyprus
| | - Chrysafis Andreou
- Department of Electrical and Computer Engineering, University of Cyprus, Nicosia 2109, Cyprus; (M.S.); (C.A.)
| | - Athos Antoniades
- Stremble Ventures Ltd., Limassol 4042, Cyprus; (P.V.); (C.B.); (A.A.)
| | | | - Yiorgos Apidianakis
- Department of Biological Sciences, University of Cyprus, Nicosia 2109, Cyprus; (K.K.); (S.T.)
- Correspondence:
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9
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Föll MC, Volkmann V, Enderle-Ammour K, Timme S, Wilhelm K, Guo D, Vitek O, Bronsert P, Schilling O. Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework. Clin Proteomics 2022; 19:8. [PMID: 35439943 PMCID: PMC9016955 DOI: 10.1186/s12014-022-09347-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
Background Mass spectrometry imaging (MSI) derives spatial molecular distribution maps directly from clinical tissue specimens and thus bears great potential for assisting pathologists with diagnostic decisions or personalized treatments. Unfortunately, progress in translational MSI is often hindered by insufficient quality control and lack of reproducible data analysis. Raw data and analysis scripts are rarely publicly shared. Here, we demonstrate the application of the Galaxy MSI tool set for the reproducible analysis of a urothelial carcinoma dataset. Methods Tryptic peptides were imaged in a cohort of 39 formalin-fixed, paraffin-embedded human urothelial cancer tissue cores with a MALDI-TOF/TOF device. The complete data analysis was performed in a fully transparent and reproducible manner on the European Galaxy Server. Annotations of tumor and stroma were performed by a pathologist and transferred to the MSI data to allow for supervised classifications of tumor vs. stroma tissue areas as well as for muscle-infiltrating and non-muscle infiltrating urothelial carcinomas. For putative peptide identifications, m/z features were matched to the MSiMass list. Results Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle infiltrating urothelial tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: stromal tissue was characterized by collagen peptides and tumor tissue by histone peptides. Immunohistochemistry confirmed an increased histone H2A abundance in the tumor compared to the stroma tissues. The muscle-infiltration status was distinguished via MSI by peptides from intermediate filaments such as cytokeratin 7 in non-muscle infiltrating carcinomas and vimentin in muscle-infiltrating urothelial carcinomas, which was confirmed by immunohistochemistry. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results via https://github.com/foellmelanie/Bladder_MSI_Manuscript_Galaxy_links. Conclusion Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.
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Affiliation(s)
- Melanie Christine Föll
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany. .,Khoury College of Computer Sciences, Northeastern University, Boston, USA.
| | - Veronika Volkmann
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany
| | - Kathrin Enderle-Ammour
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany
| | - Sylvia Timme
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany.,Core Facility for Histopathology and Digital Pathology, Faculty of Medicine, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Konrad Wilhelm
- Department of Urology, Center for Surgery, Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Dan Guo
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Peter Bronsert
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany.,Tumorbank Comprehensive Cancer Center Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Faculty of Medicine, Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106, FreiburgFreiburg, Germany.,German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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10
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Karayel-Basar M, Uras I, Kiris I, Sahin B, Akgun E, Baykal AT. Spatial proteomic alterations detected via MALDI-MS imaging implicate neuronal loss in a Huntington's disease mouse (YAC128) brain. Mol Omics 2022; 18:336-347. [PMID: 35129568 DOI: 10.1039/d1mo00440a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that occurs with the increase of CAG trinucleotide repeats in the huntingtin gene. To understand the mechanisms of HD, powerful proteomics techniques, such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) were employed. However, one major drawback of these methods is loss of the region-specific quantitative information of the proteins due to analysis of total tissue lysates. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a MS-based label-free technique that works directly on tissue sections and gathers m/z values with their respective regional information. In this study, we established a data processing protocol that includes several software programs and methods to determine spatial protein alterations between the brain samples of a 12 month-old YAC128 HD mouse model and their non-transgenic littermates. 22 differentially expressed proteins were revealed with their respective regional information, and possible relationships of several proteins were discussed. As a validation of the MALDI-MSI analysis, a differentially expressed protein (GFAP) was verified using immunohistochemical staining. Furthermore, since several proteins detected in this study have previously been associated with neuronal loss, neuronal loss in the cortical region was demonstrated using an anti-NeuN immunohistochemical staining method. In conclusion, the findings of this research have provided insights into the spatial proteomic changes between HD transgenic and non-transgenic littermates and therefore, we suggest that MALDI-MSI is a powerful technique to determine spatial proteomic alterations between biological samples, and the data processing that we present here can be employed as a complementary tool for the data analysis.
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Affiliation(s)
- Merve Karayel-Basar
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irep Uras
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Irem Kiris
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed Clinical Laboratories, R&D Center, Istanbul, Turkey
| | - Emel Akgun
- Department of Medical Biochemistry and Molecular Biology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
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11
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Zhu X, Xu T, Peng C, Wu S. Advances in MALDI Mass Spectrometry Imaging Single Cell and Tissues. Front Chem 2022; 9:782432. [PMID: 35186891 PMCID: PMC8850921 DOI: 10.3389/fchem.2021.782432] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Compared with conventional optical microscopy techniques, mass spectrometry imaging (MSI) or imaging mass spectrometry (IMS) is a powerful, label-free analytical technique, which can sensitively and simultaneously detect, quantify, and map hundreds of biomolecules, such as peptides, proteins, lipid, and other organic compounds in cells and tissues. So far, although several soft ionization techniques, such as desorption electrospray ionization (DESI) and secondary ion mass spectrometry (SIMS) have been used for imaging biomolecules, matrix-assisted laser desorption/ionization (MALDI) is still the most widespread MSI scanning method. Here, we aim to provide a comprehensive review of MALDI-MSI with an emphasis on its advances of the instrumentation, methods, application, and future directions in single cell and biological tissues.
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Affiliation(s)
- Xiaoping Zhu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianyi Xu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
- Research Center of Siyuan Natural Pharmacy and Biotoxicology, College of Life Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Shihua Wu, ; Shihua Wu,
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12
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Pillai J, Chincholkar T, Dixit R, Pandey M. A systematic review of proteomic biomarkers in oral squamous cell cancer. World J Surg Oncol 2021; 19:315. [PMID: 34711249 PMCID: PMC8555221 DOI: 10.1186/s12957-021-02423-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/06/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Head and neck squamous cell cancer (HNSCC) is the most common cancer associated with chewing tobacco, in the world. As this is divided in to sites and subsites, it does not make it to top 10 cancers. The most common subsite is the oral cancer. At the time of diagnosis, more than 50% of patients with oral squamous cell cancers (OSCC) had advanced disease, indicating the lack of availability of early detection and risk assessment biomarkers. The new protein biomarker development and discovery will aid in early diagnosis and treatment which lead to targeted treatment and ultimately a good prognosis. METHODS This systematic review was performed as per PRISMA guidelines. All relevant studies assessing characteristics of oral cancer and proteomics were considered for analysis. Only human studies published in English were included, and abstracts, incomplete articles, and cell line or animal studies were excluded. RESULTS A total of 308 articles were found, of which 112 were found to be relevant after exclusion. The present review focuses on techniques of cancer proteomics and discovery of biomarkers using these techniques. The signature of protein expression may be used to predict drug response and clinical course of disease and could be used to individualize therapy with such knowledge. CONCLUSIONS Prospective use of these markers in the clinical setting will enable early detection, prediction of response to treatment, improvement in treatment selection, and early detection of tumor recurrence for disease monitoring. However, most of these markers for OSCC are yet to be validated.
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Affiliation(s)
| | | | - Ruhi Dixit
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Manoj Pandey
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India.
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13
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Jawa Y, Yadav P, Gupta S, Mathan SV, Pandey J, Saxena AK, Kateriya S, Tiku AB, Mondal N, Bhattacharya J, Ahmad S, Chaturvedi R, Tyagi RK, Tandon V, Singh RP. Current Insights and Advancements in Head and Neck Cancer: Emerging Biomarkers and Therapeutics with Cues from Single Cell and 3D Model Omics Profiling. Front Oncol 2021; 11:676948. [PMID: 34490084 PMCID: PMC8418074 DOI: 10.3389/fonc.2021.676948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancer (HNC) is among the ten leading malignancies worldwide, with India solely contributing one-third of global oral cancer cases. The current focus of all cutting-edge strategies against this global malignancy are directed towards the heterogeneous tumor microenvironment that obstructs most treatment blueprints. Subsequent to the portrayal of established information, the review details the application of single cell technology, organoids and spheroid technology in relevance to head and neck cancer and the tumor microenvironment acknowledging the resistance pattern of the heterogeneous cell population in HNC. Bioinformatic tools are used for study of differentially expressed genes and further omics data analysis. However, these tools have several challenges and limitations when analyzing single-cell gene expression data that are discussed briefly. The review further examines the omics of HNC, through comprehensive analyses of genomics, transcriptomics, proteomics, metabolomics, and epigenomics profiles. Patterns of alterations vary between patients, thus heterogeneity and molecular alterations between patients have driven the clinical significance of molecular targeted therapies. The analyses of potential molecular targets in HNC are discussed with connotation to the alteration of key pathways in HNC followed by a comprehensive study of protein kinases as novel drug targets including its ATPase and additional binding pockets, non-catalytic domains and single residues. We herein review, the therapeutic agents targeting the potential biomarkers in light of new molecular targeted therapies. In the final analysis, this review suggests that the development of improved target-specific personalized therapies can combat HNC's global plight.
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Affiliation(s)
- Yashika Jawa
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Pooja Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Shruti Gupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sivapar V. Mathan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jyoti Pandey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ajay K. Saxena
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ashu B. Tiku
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Neelima Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh K. Tyagi
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rana P. Singh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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14
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Liu YQ, Zou HY, Xie JJ, Fang WK. Paradoxical Roles of Desmosomal Components in Head and Neck Cancer. Biomolecules 2021; 11:914. [PMID: 34203070 PMCID: PMC8234459 DOI: 10.3390/biom11060914] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 02/05/2023] Open
Abstract
Desmosomes are intercellular adhesion complexes involved in various aspects of epithelial pathophysiology, including tissue homeostasis, morphogenesis, and disease development. Recent studies have reported that the abnormal expression of various desmosomal components correlates with tumor progression and poor survival. In addition, desmosomes have been shown to act as a signaling platform to regulate the proliferation, invasion, migration, morphogenesis, and apoptosis of cancer cells. The occurrence and progression of head and neck cancer (HNC) is accompanied by abnormal expression of desmosomal components and loss of desmosome structure. However, the role of desmosomal components in the progression of HNC remains controversial. This review aims to provide an overview of recent developments showing the paradoxical roles of desmosomal components in tumor suppression and promotion. It offers valuable insights for HNC diagnosis and therapeutics development.
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Affiliation(s)
- Yin-Qiao Liu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
| | - Hai-Ying Zou
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
| | - Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, China
| | - Wang-Kai Fang
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China; (Y.-Q.L.); (H.-Y.Z.)
- Precision Medicine Research Center, Shantou University Medical College, Shantou 515041, China
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15
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Tissue-resident macrophages mediate neutrophil recruitment and kidney injury in shiga toxin-induced hemolytic uremic syndrome. Kidney Int 2021; 100:349-363. [PMID: 33930412 DOI: 10.1016/j.kint.2021.03.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 01/01/2023]
Abstract
Enterohaemorrhagic E. coli cause major epidemics worldwide with significant organ damage and very high percentages of death. Due to the ability of enterohaemorrhagic E. coli to produce shiga toxin these bacteria damage the kidney leading to the hemolytic uremic syndrome. A therapy against this serious kidney disease has not been developed yet and the impact and mechanism of leukocyte activation and recruitment are unclear. Tissue-resident macrophages represent the main leukocyte population in the healthy kidney, but the role of this important cell population in shiga toxin-producing E. coli-hemolytic uremic syndrome is incompletely understood. Using state of the art microscopy and mass spectrometry imaging, our preclinical study demonstrated a phenotypic and functional switch of tissue-resident macrophages after disease induction in mice. Kidney macrophages produced the inflammatory molecule TNFα and depletion of tissue-resident macrophages via the CSF1 receptor abolished TNFα levels in the kidney and significantly diminished disease severity. Furthermore, macrophage depletion did not only attenuate endothelial damage and thrombocytopenia, but also activation of thrombocytes and neutrophils. Moreover, we observed that neutrophils infiltrated the kidney cortex and depletion of macrophages significantly reduced the recruitment of neutrophils and expression of the neutrophil-attracting chemokines CXCL1 and CXCL2. Intravital microscopy revealed that inhibition of CXCR2, the receptor for CXCL1 and CXCL2, significantly reduced the infiltration of neutrophils and reduced kidney injury. Thus, our study shows activation of tissue-resident macrophages during shiga toxin-producing E. coli-hemolytic uremic syndrome leading to the production of disease-promoting TNFα and CXCR2-dependent recruitment of neutrophils.
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16
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Do T, Guran R, Jarosova R, Ondrackova P, Sladek Z, Faldyna M, Adam V, Zitka O. MALDI MSI Reveals the Spatial Distribution of Protein Markers in Tracheobronchial Lymph Nodes and Lung of Pigs after Respiratory Infection. Molecules 2020; 25:molecules25235723. [PMID: 33287430 PMCID: PMC7730995 DOI: 10.3390/molecules25235723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 12/17/2022] Open
Abstract
Respiratory infections are a real threat for humans, and therefore the pig model is of interest for studies. As one of a case for studies, Actinobacillus pleuropneumoniae (APP) caused infections and still worries many pig breeders around the world. To better understand the influence of pathogenic effect of APP on a respiratory system-lungs and tracheobronchial lymph nodes (TBLN), we aimed to employ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry imaging (MALDI-TOF MSI). In this study, six pigs were intranasally infected by APP and two were used as non-infected control, and 48 cryosections have been obtained. MALDI-TOF MSI and immunohistochemistry (IHC) were used to study spatial distribution of infectious markers, especially interleukins, in cryosections of porcine tissues of lungs (necrotic area, marginal zone) and tracheobronchial lymph nodes (TBLN) from pigs infected by APP. CD163, interleukin 1β (IL‑1β) and a protegrin-4 precursor were successfully detected based on their tryptic fragments. CD163 and IL‑1β were confirmed also by IHC. The protegrin-4 precursor was identified by MALDI-TOF/TOF directly on the tissue cryosections. CD163, IL‑1β and protegrin‑4 precursor were all significantly (p < 0.001) more expressed in necrotic areas of lungs infected by APP than in marginal zone, TBLN and in control lungs.
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Affiliation(s)
- Tomas Do
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic; (T.D.); (R.G.); (V.A.)
| | - Roman Guran
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic; (T.D.); (R.G.); (V.A.)
- Central European Institute of Technology, Brno University of Technology, 612 00 Brno, Czech Republic
| | - Rea Jarosova
- Department of Morphology, Physiology and Animal Genetics, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic; (R.J.); (Z.S.)
| | - Petra Ondrackova
- Department of Immunology, Veterinary Research Institute, 621 00 Brno, Czech Republic; (P.O.); (M.F.)
| | - Zbysek Sladek
- Department of Morphology, Physiology and Animal Genetics, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic; (R.J.); (Z.S.)
| | - Martin Faldyna
- Department of Immunology, Veterinary Research Institute, 621 00 Brno, Czech Republic; (P.O.); (M.F.)
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic; (T.D.); (R.G.); (V.A.)
- Central European Institute of Technology, Brno University of Technology, 612 00 Brno, Czech Republic
- Central European Institute of Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Ondrej Zitka
- Department of Chemistry and Biochemistry, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic; (T.D.); (R.G.); (V.A.)
- Central European Institute of Technology, Brno University of Technology, 612 00 Brno, Czech Republic
- Central European Institute of Technology, Mendel University in Brno, 613 00 Brno, Czech Republic
- Correspondence: ; Tel.: +420-545-133-285
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17
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Gowthami J, Gururaj N, Mahalakshmi V, Sathya R, Sabarinath TR, Doss DM. Genetic predisposition and prediction protocol for epithelial neoplasms in disease-free individuals: A systematic review. J Oral Maxillofac Pathol 2020; 24:293-307. [PMID: 33456239 PMCID: PMC7802851 DOI: 10.4103/jomfp.jomfp_348_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/23/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
Background Epithelial neoplasm is an important global health-care problem, with high morbidity and mortality rates. Early diagnosis and appropriate treatment are essential for increased life survival. Prediction of occurrence of malignancy in a disease-free individual by any means will be a great breakthrough for healthy living. Aims and Objectives The aims and objectives were to predict the genetic predisposition and propose a prediction protocol for epithelial malignancy of various systems in our body, in a disease-free individual. Methods We have searched databases both manually and electronically, published in English language in Cochrane group, Google search, MEDLINE and PubMed from 2000 to 2019. We have included all the published, peer-reviewed, narrative reviews; randomized controlled trials; case-control studies; and cohort studies and excluded the abstract-only articles and duplicates. Specific words such as "etiological factors," "pathology and mutations," "signs and symptoms," "genetics and IHC marker," and "treatment outcome" were used for the search. A total of 1032 citations were taken, and only 141 citations met the inclusion criteria and were analyzed. Results After analyzing various articles, the etiological factors, clinical signs and symptoms, genes and the pathology involved and the commonly used blood and tissue markers were analyzed. A basic investigation strategy using immunohistochemistry markers was established. Conclusion The set of proposed biomarkers should be studied in future to predict genetic predisposition in disease-free individuals.
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Affiliation(s)
- J Gowthami
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - N Gururaj
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - V Mahalakshmi
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - R Sathya
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - T R Sabarinath
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - Daffney Mano Doss
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
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18
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Arolt C, Meyer M, Hoffmann F, Wagener-Ryczek S, Schwarz D, Nachtsheim L, Beutner D, Odenthal M, Guntinas-Lichius O, Buettner R, von Eggeling F, Klußmann JP, Quaas A. Expression Profiling of Extracellular Matrix Genes Reveals Global and Entity-Specific Characteristics in Adenoid Cystic, Mucoepidermoid and Salivary Duct Carcinomas. Cancers (Basel) 2020; 12:cancers12092466. [PMID: 32878206 PMCID: PMC7564650 DOI: 10.3390/cancers12092466] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The extracellular matrix (ECM), an important factor in tumour metastasis and therapy resistance, has not been studied in salivary gland carcinomas (SGC), so far. In this retrospective study, we profiled the RNA expression of 28 ECM-related genes in 11 adenoid cystic (AdCy), 14 mucoepidermoid (MuEp) and 9 salivary duct carcinomas (SaDu). Also, we validated our results in a multimodal approach. MuEp and SaDu shared a common gene signature involving an overexpression of COL11A1. In contrast, nonhierarchical clustering revealed a more specific gene expression pattern for AdCy, characterized by overexpression of COL27A1. In situ studies at RNA level indicated that in AdCy, ECM production results from tumour cells and not from cancer-associated fibroblasts as is the case in MuEp and SaDu. For the first time, we characterized the ECM composition in SGC and identified several differentially expressed genes, which are potential therapeutic targets. Abstract The composition of the extracellular matrix (ECM) plays a pivotal role in tumour initiation, metastasis and therapy resistance. Until now, the ECM composition of salivary gland carcinomas (SGC) has not been studied. We quantitatively analysed the mRNA of 28 ECM-related genes of 34 adenoid cystic (AdCy; n = 11), mucoepidermoid (MuEp; n = 14) and salivary duct carcinomas (SaDu; n = 9). An incremental overexpression of six collagens (including COL11A1) and four glycoproteins from MuEp and SaDu suggested a common ECM alteration. Conversely, AdCy and MuEp displayed a distinct overexpression of COL27A1 and LAMB3, respectively. Nonhierarchical clustering and principal component analysis revealed a more specific pattern for AdCy with low expression of the common gene signature. In situ studies at the RNA and protein level confirmed these results and indicated that, in contrast to MuEp and SaDu, ECM production in AdCy results from tumour cells and not from cancer-associated fibroblasts (CAFs). Our findings reveal different modes of ECM production leading to common and distinct RNA signatures in SGC. Of note, an overexpression of COL27A1, as in AdCy, has not been linked to any other neoplasm so far. Here, we contribute to the dissection of the ECM composition in SGC and identified a panel of deferentially expressed genes, which could be putative targets for SGC therapy and overcoming therapeutic resistance.
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Affiliation(s)
- Christoph Arolt
- Institute of Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (S.W.-R.); (M.O.); (R.B.); (A.Q.)
- Correspondence: ; Tel.: +49-221-478-4726
| | - Moritz Meyer
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (M.M.); (D.S.); (L.N.); (J.P.K.)
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany
| | - Franziska Hoffmann
- Department of Otorhinolaryngology, MALDI Imaging and Innovative Biophotonics, Jena University Hospital, 07747 Jena, Germany;
| | - Svenja Wagener-Ryczek
- Institute of Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (S.W.-R.); (M.O.); (R.B.); (A.Q.)
| | - David Schwarz
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (M.M.); (D.S.); (L.N.); (J.P.K.)
| | - Lisa Nachtsheim
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (M.M.); (D.S.); (L.N.); (J.P.K.)
| | - Dirk Beutner
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Margarete Odenthal
- Institute of Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (S.W.-R.); (M.O.); (R.B.); (A.Q.)
| | - Orlando Guntinas-Lichius
- Department of Otorhinolaryngology, Head and Neck Surgery, Jena University Hospital, 07747 Jena, Germany;
| | - Reinhard Buettner
- Institute of Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (S.W.-R.); (M.O.); (R.B.); (A.Q.)
| | - Ferdinand von Eggeling
- Department of Otorhinolaryngology, MALDI Imaging, Core Unit Proteome Analysis, DFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL), Jena University Hospital, 07747 Jena, Germany;
| | - Jens Peter Klußmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (M.M.); (D.S.); (L.N.); (J.P.K.)
| | - Alexander Quaas
- Institute of Pathology, Medical Faculty, University of Cologne, 50937 Cologne, Germany; (S.W.-R.); (M.O.); (R.B.); (A.Q.)
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19
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Hassan MIA, Kruse JM, Krüger T, Dahse HM, Cseresnyés Z, Blango MG, Slevogt H, Hörhold F, Ast V, König R, Figge MT, Kniemeyer O, Brakhage AA, Voigt K. Functional surface proteomic profiling reveals the host heat-shock protein A8 as a mediator of Lichtheimia corymbifera recognition by murine alveolar macrophages. Environ Microbiol 2020; 22:3722-3740. [PMID: 32583550 DOI: 10.1111/1462-2920.15140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/11/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Mucormycosis is an emergent, fatal fungal infection of humans and warm-blooded animals caused by species of the order Mucorales. Immune cells of the innate immune system serve as the first line of defence against inhaled spores. Alveolar macrophages were challenged with the mucoralean fungus Lichtheimia corymbifera and subjected to biotinylation and streptavidin enrichment procedures followed by LC-MS/MS analyses. A total of 28 host proteins enriched for binding to macrophage-L. corymbifera interaction. Among those, the HSP70-family protein Hspa8 was found to be predominantly responsive to living and heat-killed spores of a virulent and an attenuated strain of L. corymbifera. Confocal scanning laser microscopy of infected macrophages revealed colocalization of Hspa8 with phagocytosed spores of L. corymbifera. The amount of detectable Hspa8 was dependent on the multiplicity of infection. Incubation of alveolar macrophages with an anti-Hspa8 antibody prior to infection reduced their capability to phagocytose spores of L. corymbifera. In contrast, anti-Hspa8 antibodies did not abrogate the phagocytosis of Aspergillus fumigatus conidia by macrophages. These results suggest an important contribution of the heat-shock family protein Hspa8 in the recognition of spores of the mucoralean fungus L. corymbifera by host alveolar macrophages and define a potential immunomodulatory therapeutic target.
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Affiliation(s)
- Mohamed I Abdelwahab Hassan
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Pests and Plant Protection Department, National Research Centre, 33rd El Buhouth St., Dokki, Giza, 12622, Egypt
| | - Janis M Kruse
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Zoltán Cseresnyés
- Department of Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Matthew G Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Hortense Slevogt
- Host Septomics Group, Centre for Innovation Competence (ZIK) Septomics, University Hospital Jena, Jena, Germany
| | - Franziska Hörhold
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Marc Thilo Figge
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Axel A Brakhage
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.,Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Kerstin Voigt
- Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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20
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Eggeling F, Hoffmann F. Microdissection—An Essential Prerequisite for Spatial Cancer Omics. Proteomics 2020; 20:e2000077. [DOI: 10.1002/pmic.202000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ferdinand Eggeling
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
| | - Franziska Hoffmann
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
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21
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Lu HC, Patterson NH, Judd AM, Reyzer ML, Sehn JK. Imaging Mass Spectrometry Is an Accurate Tool in Differentiating Clear Cell Renal Cell Carcinoma and Chromophobe Renal Cell Carcinoma: A Proof-of-concept Study. J Histochem Cytochem 2020; 68:403-411. [PMID: 32466698 DOI: 10.1369/0022155420931417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) are relatively common tumors that can have significant risk for mortality. Treatment and prognostication in renal cell carcinoma (RCC) are dependent upon correct histologic typing. ccRCC and chRCC are generally straightforward to diagnose based on histomorphology alone. However, high-grade ccRCC and chRCC can sometimes resemble each other morphologically, particularly in small biopsies. Multiple immunostains and/or colloidal iron stain are sometimes required to differentiate the two. Imaging mass spectrometry (IMS) allows simultaneous spatial mapping of thousands of biomarkers, using formalin-fixed paraffin-embedded tissue sections. In this study, we evaluate the ability of IMS to differentiate between World Health Organization/International Society for Urological Pathology grade 3 ccRCC and chRCC. IMS spectra from a training set of 14 ccRCC and 13 chRCC were evaluated via support vector machine algorithm with a linear kernel for machine learning, building a classification model. The classification model was applied to a separate validation set of 6 ccRCC and 6 chRCC, with 19 to 20, 150-μm diameter tumor foci in each case sampled by IMS. Most evaluated tumor foci were classified correctly as ccRCC versus chRCC (99% accuracy, kappa=0.98), demonstrating that IMS is an accurate tool in differentiating high-grade ccRCC and chRCC.
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Affiliation(s)
- Hsiang-Chih Lu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Audra M Judd
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Michelle L Reyzer
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN
| | - Jennifer K Sehn
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO
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22
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Macklin A, Khan S, Kislinger T. Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin Proteomics 2020; 17:17. [PMID: 32489335 PMCID: PMC7247207 DOI: 10.1186/s12014-020-09283-w] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method that enables increasingly comprehensive insights into changes of the proteome to advance personalized medicine. In this review, recent improvements in MS-based clinical proteomics are highlighted with a focus on oncology. We will provide a detailed overview of clinically relevant samples types, as well as, consideration for sample preparation methods, protein quantitation strategies, MS configurations, and data analysis pipelines currently available to researchers. Critical consideration of each step is necessary to address the pressing clinical questions that advance cancer patient diagnosis and prognosis. While the majority of studies focus on the discovery of clinically-relevant biomarkers, there is a growing demand for rigorous biomarker validation. These studies focus on high-throughput targeted MS assays and multi-centre studies with standardized protocols. Additionally, improvements in MS sensitivity are opening the door to new classes of tumour-specific proteoforms including post-translational modifications and variants originating from genomic aberrations. Overlaying proteomic data to complement genomic and transcriptomic datasets forges the growing field of proteogenomics, which shows great potential to improve our understanding of cancer biology. Overall, these advancements not only solidify MS-based clinical proteomics' integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.
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Affiliation(s)
- Andrew Macklin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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23
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Spatial proteomics revealed a CX 3CL1-dependent crosstalk between the urothelium and relocated macrophages through IL-6 during an acute bacterial infection in the urinary bladder. Mucosal Immunol 2020; 13:702-714. [PMID: 32112048 PMCID: PMC7312419 DOI: 10.1038/s41385-020-0269-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 02/04/2023]
Abstract
The urothelium of the urinary bladder represents the first line of defense. However, uropathogenic E. coli (UPEC) damage the urothelium and cause acute bacterial infection. Here, we demonstrate the crosstalk between macrophages and the urothelium stimulating macrophage migration into the urothelium. Using spatial proteomics by MALDI-MSI and LC-MS/MS, a novel algorithm revealed the spatial activation and migration of macrophages. Analysis of the spatial proteome unravelled the coexpression of Myo9b and F4/80 in the infected urothelium, indicating that macrophages have entered the urothelium upon infection. Immunofluorescence microscopy additionally indicated that intraurothelial macrophages phagocytosed UPEC and eliminated neutrophils. Further analysis of the spatial proteome by MALDI-MSI showed strong expression of IL-6 in the urothelium and local inhibition of this molecule reduced macrophage migration into the urothelium and aggravated the infection. After IL-6 inhibition, the expression of matrix metalloproteinases and chemokines, such as CX3CL1 was reduced in the urothelium. Accordingly, macrophage migration into the urothelium was diminished in the absence of CX3CL1 signaling in Cx3cr1gfp/gfp mice. Conclusively, this study describes the crosstalk between the infected urothelium and macrophages through IL-6-induced CX3CL1 expression. Such crosstalk facilitates the relocation of macrophages into the urothelium and reduces bacterial burden in the urinary bladder.
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24
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Thielker J, Weise A, Othman MAK, Carreria IM, Melo JB, Von Eggeling F, Guntinas-Lichius O, Ziegler M, Liehr T. Molecular cytogenetic pilot study on pleomorphic adenomas of salivary glands. Oncol Lett 2019; 19:1125-1130. [PMID: 31966040 PMCID: PMC6955655 DOI: 10.3892/ol.2019.11198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/24/2019] [Indexed: 01/17/2023] Open
Abstract
Pleomorphic adenomas (PAs) of salivary glands are the most frequent entity of solid parotid tumors. Nonetheless, their genetics is not yet well understood. Thus, the current study characterized 14 PAs using a unique combination of cytogenetic, molecular cytogenetic and/or molecular karyotyping based approaches. The current study applied G-banding based on trypsin treatment and Giemsa-staining in peripheral blood and tumor tissue. Additionally, fluorescence in situ hybridization was performed using whole chromosome painting or centromeric probes. Array-based comparative genomic hybridization was also conducted. In 5 of 14 cases, chromosomal and/or submicroscopic alterations were characterized. Balanced and unbalanced translocations, loss or gain of whole chromosomes and submicroscopic copy number alterations were detected. Furthermore, the first case of a so-called ‘jumping translocation’ in a PA was reported. The genes twist-related protein 1 and distal-less homeobox 5 were also involved in copy number variations in two PAs. In conclusion, approaches utilized in the current study are highly suited to characterize the genetic constitution of PAs.
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Affiliation(s)
- Jovanna Thielker
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Moneeb A K Othman
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Isabel M Carreria
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal.,The Center of Investigation On Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal.,The Center of Investigation On Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Polo Ciências da Saúde, Coimbra 3000-354, Portugal
| | - Ferdinand Von Eggeling
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, D-07743 Jena, Germany
| | - Orlando Guntinas-Lichius
- Department of Otorhinolaryngology, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Monika Ziegler
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07747 Jena, Germany
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25
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Buzdin A, Sorokin M, Garazha A, Glusker A, Aleshin A, Poddubskaya E, Sekacheva M, Kim E, Gaifullin N, Giese A, Seryakov A, Rumiantsev P, Moshkovskii S, Moiseev A. RNA sequencing for research and diagnostics in clinical oncology. Semin Cancer Biol 2019; 60:311-323. [PMID: 31412295 DOI: 10.1016/j.semcancer.2019.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022]
Abstract
Molecular diagnostics is becoming one of the major drivers of personalized oncology. With hundreds of different approved anticancer drugs and regimens of their administration, selecting the proper treatment for a patient is at least nontrivial task. This is especially sound for the cases of recurrent and metastatic cancers where the standard lines of therapy failed. Recent trials demonstrated that mutation assays have a strong limitation in personalized selection of therapeutics, consequently, most of the drugs cannot be ranked and only a small percentage of patients can benefit from the screening. Other approaches are, therefore, needed to address a problem of finding proper targeted therapies. The analysis of RNA expression (transcriptomic) profiles presents a reasonable solution because transcriptomics stands a few steps closer to tumor phenotype than the genome analysis. Several recent studies pioneered using transcriptomics for practical oncology and showed truly encouraging clinical results. The possibility of directly measuring of expression levels of molecular drugs' targets and profiling activation of the relevant molecular pathways enables personalized prioritizing for all types of molecular-targeted therapies. RNA sequencing is the most robust tool for the high throughput quantitative transcriptomics. Its use, potentials, and limitations for the clinical oncology will be reviewed here along with the technical aspects such as optimal types of biosamples, RNA sequencing profile normalization, quality controls and several levels of data analysis.
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Affiliation(s)
- Anton Buzdin
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Omicsway Corp., Walnut, CA, USA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Maxim Sorokin
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Omicsway Corp., Walnut, CA, USA; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Alex Aleshin
- Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Elena Poddubskaya
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia; Vitamed Oncological Clinics, Moscow, Russia
| | - Marina Sekacheva
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Ella Kim
- Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nurshat Gaifullin
- Lomonosov Moscow State University, Faculty of Medicine, Moscow, Russia
| | | | | | | | - Sergey Moshkovskii
- Institute of Biomedical Chemistry, Moscow, 119121, Russia; Pirogov Russian National Research Medical University (RNRMU), Moscow, 117997, Russia
| | - Alexey Moiseev
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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26
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Ahmed M, Broeckx G, Baggerman G, Schildermans K, Pauwels P, Van Craenenbroeck AH, Dendooven A. Next-generation protein analysis in the pathology department. J Clin Pathol 2019; 73:1-6. [DOI: 10.1136/jclinpath-2019-205864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/12/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023]
Abstract
Traditionally, immunohistochemistry (IHC) is used by pathologists to localise specific proteins or peptides in tissue slides. In the era of personalised medicine, however, molecular tissue analysis becomes indispensable for correct diagnosis, prognosis and therapeutic decision, not only on the DNA or mRNA level but also on the protein level. Combining molecular information with imaging presents many advantages. Therefore, matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) is a promising technique to be added to the armamentarium of the pathologist. Here, we focus on the workflow, advantages and drawbacks of both MALDI IMS and IHC. We also briefly discuss a few other protein imaging modalities and give examples of applications.
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27
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Giusti L, Angeloni C, Lucacchini A. Update on proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2019; 16:513-520. [DOI: 10.1080/14789450.2019.1615452] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Laura Giusti
- School of Pharmacy, University of Camerino, Camerino, Italy
| | | | - Antonio Lucacchini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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28
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Longuespée R, Casadonte R, Schwamborn K, Kriegsmann M. Proteomics in Pathology: The Special Issue. Proteomics Clin Appl 2019; 13:e1800167. [PMID: 30730117 DOI: 10.1002/prca.201800167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Rémi Longuespée
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Kristina Schwamborn
- Institute of Pathology, Technical University of Munich, 81675, Munich, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
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