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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kaczmarek MM, Myszczyński K, Kiśluk J, Majewska A, Michalska-Falkowska A, Kodzik N, Reszeć J, Sierko E, Nikliński J. Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype. PLoS One 2022; 17:e0268073. [PMID: 35512017 PMCID: PMC9071164 DOI: 10.1371/journal.pone.0268073] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Monika M. Kaczmarek
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Majewska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Natalia Kodzik
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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Čermák V, Škarková A, Merta L, Kolomazníková V, Palušová V, Uldrijan S, Rösel D, Brábek J. RNA-seq Characterization of Melanoma Phenotype Switch in 3D Collagen after p38 MAPK Inhibitor Treatment. Biomolecules 2021; 11:biom11030449. [PMID: 33802847 PMCID: PMC8002814 DOI: 10.3390/biom11030449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Melanoma phenotype plasticity underlies tumour dissemination and resistance to therapy, yet its regulation is incompletely understood. In vivo switching between a more differentiated, proliferative phenotype and a dedifferentiated, invasive phenotype is directed by the tumour microenvironment. We found that treatment of partially dedifferentiated, invasive A375M2 cells with two structurally unrelated p38 MAPK inhibitors, SB2021920 and BIRB796, induces a phenotype switch in 3D collagen, as documented by increased expression of melanocyte differentiation markers and a loss of invasive phenotype markers. The phenotype is accompanied by morphological change corresponding to amoeboid–mesenchymal transition. We performed RNA sequencing with an Illumina HiSeq platform to fully characterise transcriptome changes underlying the switch. Gene expression results obtained with RNA-seq were validated by comparing them with RT-qPCR. Transcriptomic data generated in the study will extend the present understanding of phenotype plasticity in melanoma and its contribution to invasion and metastasis.
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Affiliation(s)
- Vladimír Čermák
- Department of Cell Biology, Charles University, Viničná 7, 128 44 Prague, Czech Republic; (V.Č.); (A.Š.); (L.M.); (V.K.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 252 42 Vestec u Prahy, Czech Republic
| | - Aneta Škarková
- Department of Cell Biology, Charles University, Viničná 7, 128 44 Prague, Czech Republic; (V.Č.); (A.Š.); (L.M.); (V.K.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 252 42 Vestec u Prahy, Czech Republic
| | - Ladislav Merta
- Department of Cell Biology, Charles University, Viničná 7, 128 44 Prague, Czech Republic; (V.Č.); (A.Š.); (L.M.); (V.K.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 252 42 Vestec u Prahy, Czech Republic
| | - Veronika Kolomazníková
- Department of Cell Biology, Charles University, Viničná 7, 128 44 Prague, Czech Republic; (V.Č.); (A.Š.); (L.M.); (V.K.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 252 42 Vestec u Prahy, Czech Republic
| | - Veronika Palušová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (V.P.); (S.U.)
- International Clinical Research Center, St. Anne’s University Hospital, Pekařská 53, 656 91 Brno, Czech Republic
| | - Stjepan Uldrijan
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (V.P.); (S.U.)
- International Clinical Research Center, St. Anne’s University Hospital, Pekařská 53, 656 91 Brno, Czech Republic
| | - Daniel Rösel
- Department of Cell Biology, Charles University, Viničná 7, 128 44 Prague, Czech Republic; (V.Č.); (A.Š.); (L.M.); (V.K.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 252 42 Vestec u Prahy, Czech Republic
| | - Jan Brábek
- Department of Cell Biology, Charles University, Viničná 7, 128 44 Prague, Czech Republic; (V.Č.); (A.Š.); (L.M.); (V.K.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 252 42 Vestec u Prahy, Czech Republic
- Correspondence: ; Tel./Fax: +420-3258-73900
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Single-Cell RNA Sequencing Unravels Heterogeneity of the Stromal Niche in Cutaneous Melanoma Heterogeneous Spheroids. Cancers (Basel) 2020; 12:cancers12113324. [PMID: 33182777 PMCID: PMC7697260 DOI: 10.3390/cancers12113324] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous spheroids have recently acquired a prominent position in melanoma research because they incorporate microenvironmental cues relevant for melanoma. In this study, we focused on the analysis of microenvironmental factors introduced in melanoma heterogeneous spheroids by different dermal fibroblasts. We aimed to map the fibroblast diversity resulting from previously acquired damage caused by exposure to extrinsic and intrinsic stimuli. To construct heterogeneous melanoma spheroids, we used normal dermal fibroblasts from the sun-protected skin of a juvenile donor. We compared them to the fibroblasts from the sun-exposed photodamaged skin of an adult donor. Further, we analysed the spheroids by single-cell RNA sequencing. To validate transcriptional data, we also compared the immunohistochemical analysis of heterogeneous spheroids to melanoma biopsies. We have distinguished three functional clusters in primary human fibroblasts from melanoma spheroids. These clusters differed in the expression of (a) extracellular matrix-related genes, (b) pro-inflammatory factors, and (c) TGFβ signalling superfamily. We observed a broader deregulation of gene transcription in previously photodamaged cells. We have confirmed that pro-inflammatory cytokine IL-6 significantly enhances melanoma invasion to the extracellular matrix in our model. This supports the opinion that the aspects of ageing are essential for reliable melanoma 3D modelling in vitro.
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Gandalovičová A, Šůchová AM, Čermák V, Merta L, Rösel D, Brábek J. Sustained Inflammatory Signalling through Stat1/Stat2/IRF9 Is Associated with Amoeboid Phenotype of Melanoma Cells. Cancers (Basel) 2020; 12:cancers12092450. [PMID: 32872349 PMCID: PMC7564052 DOI: 10.3390/cancers12092450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 01/26/2023] Open
Abstract
Simple Summary Treatment of metastatic cancer is complicated by the ability of cancer cells to utilize various invasion modes when spreading through the body. Here, we studied the transition of melanoma cells between the round, amoeboid and elongated, mesenchymal invasion modes. Our results show that inflammatory signalling, which is commonly upregulated in the tumour microenvironment, is associated with the amoeboid phenotype of cancer cells. Treatment of melanoma cells with interferon beta promotes the amoeboid invasion modes and individual invasion. This suggests that inflammation associated signalling contributes to cancer cell invasion plasticity. Abstract The invasive behaviour of cancer cells underlies metastatic dissemination; however, due to the large plasticity of invasion modes, it is challenging to target. It is now widely accepted that various secreted cytokines modulate the tumour microenvironment and pro-inflammatory signalling can promote tumour progression. Here, we report that cells after mesenchymal–amoeboid transition show the increased expression of genes associated with the type I interferon response. Moreover, the sustained activation of type I interferon signalling in response to IFNβ mediated by the Stat1/Stat2/IRF9 complex enhances the round amoeboid phenotype in melanoma cells, whereas its downregulation by various approaches promotes the mesenchymal invasive phenotype. Overall, we demonstrate that interferon signalling is associated with the amoeboid phenotype of cancer cells and suggest a novel role of IFNβ in promoting cancer invasion plasticity, aside from its known role as a tumour suppressor.
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Affiliation(s)
- Aneta Gandalovičová
- Department of Cell Biology, Charles University, 12843 Prague, Czech Republic; (A.G.); (A.-M.Š.); (V.Č.); (L.M.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), 25242 Vestec, Czech Republic
| | - Anna-Marie Šůchová
- Department of Cell Biology, Charles University, 12843 Prague, Czech Republic; (A.G.); (A.-M.Š.); (V.Č.); (L.M.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), 25242 Vestec, Czech Republic
| | - Vladimír Čermák
- Department of Cell Biology, Charles University, 12843 Prague, Czech Republic; (A.G.); (A.-M.Š.); (V.Č.); (L.M.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), 25242 Vestec, Czech Republic
| | - Ladislav Merta
- Department of Cell Biology, Charles University, 12843 Prague, Czech Republic; (A.G.); (A.-M.Š.); (V.Č.); (L.M.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), 25242 Vestec, Czech Republic
| | - Daniel Rösel
- Department of Cell Biology, Charles University, 12843 Prague, Czech Republic; (A.G.); (A.-M.Š.); (V.Č.); (L.M.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), 25242 Vestec, Czech Republic
| | - Jan Brábek
- Department of Cell Biology, Charles University, 12843 Prague, Czech Republic; (A.G.); (A.-M.Š.); (V.Č.); (L.M.); (D.R.)
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), 25242 Vestec, Czech Republic
- Correspondence: or
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