Identifications of novel mechanisms in breast cancer cells involving duct-like multicellular spheroid formation after exposure to the Random Positioning Machine

Kopp, Sascha; Slumstrup, Lasse; Corydon, Thomas J.; Sahana, Jayashree; Aleshcheva, Ganna; Islam, Tawhidul; Magnusson, Nils E.; Wehland, Markus; Bauer, Johann; Infanger, Manfred; Grimm, Daniela

doi:10.1038/srep26887

Cited by 73 publications

(122 citation statements)

References 97 publications

(221 reference statements)

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“…EGFR is a well-known growth factor receptor noted for its critical role on cell division control. Moreover, three top genes EZR (ranked 12th), TUBB (ranked 27th), and RDX (ranked 36th), were shown to be involved in organization and regulation of morphological characteristics of breast cancer cells including cell shape and membrane to membrane docking (Kopp et al, 2016). …”

Section: Resultsmentioning

confidence: 99%

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

Zhu

Ching

Pan

et al. 2017

PeerJ

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Single-cell RNA-Sequencing (scRNA-Seq) is a fast-evolving technology that enables the understanding of biological processes at an unprecedentedly high resolution. However, well-suited bioinformatics tools to analyze the data generated from this new technology are still lacking. Here we investigate the performance of non-negative matrix factorization (NMF) method to analyze a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic stem cells to human glioblastoma data. In comparison to other unsupervised clustering methods including K-means and hierarchical clustering, NMF has higher accuracy in separating similar groups in various datasets. We ranked genes by their importance scores (D-scores) in separating these groups, and discovered that NMF uniquely identifies genes expressed at intermediate levels as top-ranked genes. Finally, we show that in conjugation with the modularity detection method FEM, NMF reveals meaningful protein-protein interaction modules. In summary, we propose that NMF is a desirable method to analyze heterogeneous single-cell RNA-Seq data. The NMF based subpopulation detection package is available at: https://github.com/lanagarmire/NMFEM.

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Section: Resultsmentioning

confidence: 99%

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

Zhu

Ching

Pan

et al. 2017

PeerJ

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“…Interleukin-8 (IL-8) plays an important role in 3D growth and spheroid formation of cancer cells and benign cells [20, 31, 32]. Therefore, we focused on IL-8 in these experiments.…”

Section: Resultsmentioning

confidence: 99%

“…6F). Furthermore, NGAL had been detected in different cancer types [25, 31]. Its role in 3D growth of ECs has to be studied in more detail in the future.…”

Section: Discussionmentioning

confidence: 99%

Key Proteins Involved in Spheroid Formation and Angiogenesis in Endothelial Cells After Long-Term Exposure to Simulated Microgravity

Dittrich

Grimm

Sahana

et al. 2018

Cell Physiol Biochem

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Background/Aims: Cardiovascular complications are common in astronauts returning from a prolonged spaceflight. These health problems might be driven by complex modulations of gene expression and protein synthesis in endothelial cells (ECs). Studies on the influence of microgravity on phenotype, growth pattern and biological processes of ECs can help to understand these complications. Methods: We exposed ECs (EA.hy926) to a Random Positioning Machine (RPM). Proteins associated with cell structure, angiogenesis and endothelial dysfunction were investigated in distinct pools of multicellular spheroids (MCS), adherent cells (AD) and tubular structures (TS) formed after a 35-day RPM-exposure. Results: Combining morphological and molecular approaches, we found AD, MCS and TS with changes in the synthesis and release of proteins involved in three-dimensional growth. Fibronectin and monocyte chemoattractant protein-1 (MCP-1) mRNAs and protein contents were elevated along with an increased secretion of vascular endothelial growth factor (VEGF), interleukin (IL)-6, IL-8, MCP-1, intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), neutrophil gelatinase-associated lipocalin (NGAL) and regulated on activation, normal T cell expressed and secreted (RANTES) proteins in the culture supernatant as determined by multianalyte profiling technology. Together they form a network of interaction. Conclusions: These results show that a prolonged RPM-exposure of ECs induced TS and MCS formation. The factors VEGF, NGAL, IL-6, IL-8, MCP-1, VCAM-1, ICAM-1, fibronectin and RANTES seem to be affected when gravity is omitted.

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“…Whole cell lysates were used for Western blotting following routine protocols for gel electrophoresis and trans-blotting, as described earlier [31, 33]. Equal amounts of 10 µL lysate containing 2 µg/µL protein were loaded on precast TGX stain-free gels (Bio-Rad, Munich, Germany).…”

Section: Methodsmentioning

confidence: 99%

“…For the analysis, SwissProt numbers of the investigated proteins were entered and networks built by the software based on relationships and processes from the literature, PubMed, databases and experimental data [9, 10, 33]. …”

Section: Methodsmentioning

confidence: 99%

Cytokine Release and Focal Adhesion Proteins in Normal Thyroid Cells Cultured on the Random Positioning Machine

Warnke

Pietsch

Kopp

et al. 2017

Cell Physiol Biochem

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Background/Aims: Spaceflight impacts on the function of the thyroid gland in vivo. In vitro normal and malignant thyrocytes assemble in part to multicellular spheroids (MCS) after exposure to the random positioning machine (RPM), while a number of cells remain adherent (AD). We aim to elucidate possible differences between AD and MCS cells compared to 1g-controls of normal human thyroid cells. Methods: Cells of the human follicular epithelial thyroid cell line Nthy-ori 3-1 were incubated for up to 72 h on the RPM. Afterwards, they were investigated by phase-contrast microscopy, quantitative real-time PCR and by determination of cytokines released in their supernatants. Results: A significant up-regulation of IL6, IL8 and CCL2 gene expression was found after a 4h RPM-exposure, when the whole population was still growing adherently. MCS and AD cells were detected after 24 h on the RPM. At this time, a significantly reduced gene expression in MCS compared to 1g-controls was visible for IL6, IL8, FN1, ITGB1, LAMA1, CCL2, and TLN1. After a 72 h RPM-exposure, IL-6, IL-8, and TIMP-1 secretion rates were increased significantly. Conclusion: Normal thyrocytes form MCS within 24 h. Cytokines seem to be involved in the initiation of MCS formation via focal adhesion proteins.

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Identifications of novel mechanisms in breast cancer cells involving duct-like multicellular spheroid formation after exposure to the Random Positioning Machine

Cited by 73 publications

References 97 publications

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

Key Proteins Involved in Spheroid Formation and Angiogenesis in Endothelial Cells After Long-Term Exposure to Simulated Microgravity

Cytokine Release and Focal Adhesion Proteins in Normal Thyroid Cells Cultured on the Random Positioning Machine

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