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Pasternack H, Polzer M, Gemoll T, Kümpers C, Sauer T, Lazar-Karsten P, Hinrichs S, Bohnet S, Perner S, Dressler FF, Kirfel J. Proteomic analyses identify HK1 and ATP5A to be overexpressed in distant metastases of lung adenocarcinomas compared to matched primary tumors. Sci Rep 2023; 13:20948. [PMID: 38016997 PMCID: PMC10684588 DOI: 10.1038/s41598-023-47767-5] [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: 06/30/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide with lung adenocarcinoma (LUAD) being the most common type. Genomic studies of LUAD have advanced our understanding of its tumor biology and accelerated targeted therapy. However, the proteomic characteristics of LUAD are still insufficiently explored. The prognosis for lung cancer patients is still mostly determined by the stage of disease at the time of diagnosis. Focusing on late-stage metastatic LUAD with poor prognosis, we compared the proteomic profiles of primary tumors and matched distant metastases to identify relevant and potentially druggable differences. We performed high-performance liquid chromatography (HPLC) and electrospray ionization tandem mass spectrometry (ESI-MS/MS) on a total of 38 FFPE (formalin-fixed and paraffin-embedded) samples. Using differential expression analysis and unsupervised clustering we identified several proteins that were differentially regulated in metastases compared to matched primary tumors. Selected proteins (HK1, ATP5A, SRI and ARHGDIB) were subjected to validation by immunoblotting. Thereby, significant differential expression could be confirmed for HK1 and ATP5A, both upregulated in metastases compared to matched primary tumors. Our findings give a better understanding of tumor progression and metastatic spreads in LUAD but also demonstrate considerable inter-individual heterogeneity on the proteomic level.
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Affiliation(s)
- Helen Pasternack
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Mirjam Polzer
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Institute of Legal Medicine, University Hospital Münster, Münster, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Christiane Kümpers
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Thorben Sauer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Pamela Lazar-Karsten
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sofie Hinrichs
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sabine Bohnet
- Department of Pulmonology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sven Perner
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Institute of Pathology and Hematopathology, Hamburg, Germany
| | - Franz Friedrich Dressler
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Institute of Pathology, Charité -Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jutta Kirfel
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.
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Burns JS, Kassem M. Identifying Biomarkers for Osteogenic Potency Assay Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1420:39-58. [PMID: 37258783 DOI: 10.1007/978-3-031-30040-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
There has been extensive exploration of how cells may serve as advanced therapy medicinal products to treat skeletal pathologies. Osteoblast progenitors responsible for production of extracellular matrix that is subsequently mineralized during bone formation have been characterised as a rare bone marrow subpopulation of cell culture plastic adherent cells. Conveniently, they proliferate to form single-cell derived colonies of fibroblastoid cells, termed colony forming unit fibroblasts that can subsequently differentiate to aggregates resembling small areas of cartilage or bone. However, donor heterogeneity and loss of osteogenic differentiation capacity during extended cell culture have made the discovery of reliable potency assay biomarkers difficult. Nonetheless, functional osteoblast models derived from telomerised human bone marrow stromal cells have allowed extensive comparative analysis of gene expression, microRNA, morphological phenotypes and secreted proteins. This chapter highlights numerous insights into the molecular mechanisms underpinning osteogenic differentiation of multipotent stromal cells and bone formation, discussing aspects involved in the choice of useful biomarkers for functional attributes that can be quantitively measured in osteogenic potency assays.
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Affiliation(s)
- Jorge S Burns
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy.
| | - Moustapha Kassem
- University Hospital of Odense, University of Southern Denmark, Odense, Denmark
- Danish Stem Cell Center, University of Copenhagen, Copenhagen, Denmark
- College of Medicine, King Saud University, Riyadh, Saudi Arabia
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Daprà V, Alotto D, Casarin S, Gambarino S, Zavatto C, Dini M, Galliano I, Castagnoli C, Bergallo M. A new protocol for validation of Chondro, Adipo and Osteo differentiation kit of Cultured Adipose-Derived Stem Cells (ADSC) by real-time rt-QPCR. Tissue Cell 2022; 79:101923. [DOI: 10.1016/j.tice.2022.101923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 10/14/2022]
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Yasamineh S, Kalajahi HG, Yasamineh P, Gholizadeh O, Youshanlouei HR, Matloub SK, Mozafari M, Jokar E, Yazdani Y, Dadashpour M. Spotlight on therapeutic efficiency of mesenchymal stem cells in viral infections with a focus on COVID-19. Stem Cell Res Ther 2022; 13:257. [PMID: 35715852 PMCID: PMC9204679 DOI: 10.1186/s13287-022-02944-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/02/2022] [Indexed: 11/21/2022] Open
Abstract
The SARS-COV-2 virus has infected the world at a very high rate by causing COVID-19 disease. Nearly 507 million individuals have been infected with this virus, with approximately 1.2% of these patients being dead, indicating that this virus has been out of control in many countries. While researchers are investigating how to develop efficient drugs and vaccines versus the COVID-19 pandemic, new superseded treatments have the potential to reduce mortality. The recent application of mesenchymal stem cells (MSCs) in a subgroup of COVID-19 patients with acute respiratory distress has created potential benefits as supportive therapy for this viral contagion in patients with acute conditions and aged patients with severe pneumonia. Consequently, within this overview, we discuss the role and therapeutic potential of MSCs and the challenges ahead in using them to treat viral infections, with highlighting on COVID-19 infection.
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Affiliation(s)
- Saman Yasamineh
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Pooneh Yasamineh
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Omid Gholizadeh
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Rahmani Youshanlouei
- Department of Internal Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Masoud Mozafari
- Cardiovascular Pharmacology Research Lab, Department of Pharmacology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elham Jokar
- Department of Medical Chemistry, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Yalda Yazdani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mehdi Dadashpour
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran.
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Protein Profiling of WERI-RB1 and Etoposide-Resistant WERI-ETOR Reveals New Insights into Topoisomerase Inhibitor Resistance in Retinoblastoma. Int J Mol Sci 2022; 23:ijms23074058. [PMID: 35409416 PMCID: PMC9000009 DOI: 10.3390/ijms23074058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/23/2022] [Accepted: 04/02/2022] [Indexed: 12/16/2022] Open
Abstract
Chemotherapy resistance is one of the reasons for eye loss in patients with retinoblastoma (RB). RB chemotherapy resistance has been studied in different cell culture models, such as WERI-RB1. In addition, chemotherapy-resistant RB subclones, such as the etoposide-resistant WERI-ETOR cell line have been established to improve the understanding of chemotherapy resistance in RB. The objective of this study was to characterize cell line models of an etoposide-sensitive WERI-RB1 and its etoposide-resistant subclone, WERI-ETOR, by proteomic analysis. Subsequently, quantitative proteomics data served for correlation analysis with known drug perturbation profiles. Methodically, WERI-RB1 and WERI-ETOR were cultured, and prepared for quantitative mass spectrometry (MS). This was carried out in a data-independent acquisition (DIA) mode. The raw SWATH (sequential window acquisition of all theoretical mass spectra) files were processed using neural networks in a library-free mode along with machine-learning algorithms. Pathway-enrichment analysis was performed using the REACTOME-pathway resource, and correlated to the molecular signature database (MSigDB) hallmark gene set collections for functional annotation. Furthermore, a drug-connectivity analysis using the L1000 database was carried out to associate the mechanism of action (MOA) for different anticancer reagents to WERI-RB1/WERI-ETOR signatures. A total of 4756 proteins were identified across all samples, showing a distinct clustering between the groups. Of these proteins, 64 were significantly altered (q < 0.05 & log2FC |>2|, 22 higher in WERI-ETOR). Pathway analysis revealed the “retinoid metabolism and transport” pathway as an enriched metabolic pathway in WERI-ETOR cells, while the “sphingolipid de novo biosynthesis” pathway was identified in the WERI-RB1 cell line. In addition, this study revealed similar protein signatures of topoisomerase inhibitors in WERI-ETOR cells as well as ATPase inhibitors, acetylcholine receptor antagonists, and vascular endothelial growth factor receptor (VEGFR) inhibitors in the WERI-RB1 cell line. In this study, WERI-RB1 and WERI-ETOR were analyzed as a cell line model for chemotherapy resistance in RB using data-independent MS. Analysis of the global proteome identified activation of “sphingolipid de novo biosynthesis” in WERI-RB1, and revealed future potential treatment options for etoposide resistance in RB.
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