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Additional file 11: Table S8. Clusters of the metabolites of 45 experiments originating of 15 young individuals.

Head and neck squamous cell carcinoma (HNSCC) is a highly malignant disease with a mortality rate of about 50%. It represents the sixth most common type of malignant tumor in the world. Risk factors include tobacco and alcohol usage and infection with the human papilloma virus (HPV). HPV-negative HNSCCs frequently display areas of cornification evident by keratin pearls in the tumor tissue. Cornification represents a natural differentiation path of keratinocytes in the normal epidermis and oral mucosa. To investigate the mechanisms of HNSCC cell differentiation we have established spheroid cell cultures from patient-derived HNSCC and parotid gland adenoid cystic carcinoma (ACC) tissue that grow in suspension under serum-free conditions. The use of a specific differentiation medium induced striking adhesion, loss of proliferation, and differentiation in tumor cells. Spheroid cells grew as single cell clones under serum-free conditions with a cloning efficiency of 40-60%, which was fully diminished under differentiating conditions. HNSCC cells cornified as indicated by the formation of lamellar bodies in the cytoplasm of adherent cells and an upregulation of cornification markers SPRR3 and involucrin. ACC cells upregulated parotid gland differentiation markers including α-amylase. RNA-seq analysis in HNSCC cells confirmed an upregulation of signaling pathways associated with cornification and epithelial cell differentiation. Conversely, pathways regulating the three-dimensional organization of the genome were downregulated upon differentiation. This was accompanied by the formation of ATRX-positive heterochromatin foci in the nucleus of differentiated ACC and HNSCC cells resembling those previously described to arise during therapy-induced senescence. Moreover, gas chromatography mass spectrometry analysis revealed a lack of essential amino acids including leucine to be implicated in the differentiation process. Altogether, our spheroid model of HNSCC and ACC cells is suitable to analyze the mechanisms underlying tumor cell differentiation and might lead to new therapeutic approaches that can drive long-term repopulating HNSCC and ACC cells into differentiation. Citation Format: Felix Oppel, Senyao Shao, Sarah Gendreizig, Philipp Kühnel, Vivien Przybycin, Carsten Hain, Pascal Schmidt, Matthias Schürmann, Peter Goon, Karsten Niehaus, Jörn Kalinowski, Holger Sudhoff. Head and neck cancer cells can differentiate and resemble their tissue of origin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 111.

Additional file 5: Table S2. List of the parameters and their values that are used in the KNIME workflow for the map alignment (correcting retention time distortions between maps).

Additional file 6: Table S3. List of the parameters and their values that are used in the KNIME workflow for grouping corresponding features from multiple maps.

Additional file 4: Table S1. List of the parameters and their values that are used in the KNIME workflow for assembling the metabolite features.

Additional file 9: Table S6. List of clusters and number of experiments in each one.

Additional file 7: Table S4. The study identifiers from 38 studies of the MetaboLights repository that were used for processing and analysis.

Xanthomonas campestris strains are used world-wide for the production of the industrially important exopolysaccharide xanthan. The high industrial relevance of xanthan can be explained by its extraordinary qualities as rheological control agent in aqueous systems and by its stabilizing properties in suspensions and emulsions. The phytopathogen Xanthomonas campestris is a motile bacterium with one polar flagellum. The flagellum is a cost intensive structure, in terms of energy and building block consumption. Based on the assumption that inhibition of the flagellar biosynthesis and related proton driven motility might be beneficial for the xanthan production in Xcc, two genes (fliC and fliM) were mutated to inhibit the motility. Both mutants Xcc JBL007 fliC- and Xcc JBL007 fliM- showed an increased xanthan production. Remarkably, the produced xanthan from both mutants showed enhanced rheological properties. While the chemical composition of the produced xanthan of the initial and both mutant strains did not change, notable differences in persistence length could be measured via atomic force microscopy. Results presented in this study demonstrate the possibility to further improve the xanthan production by Xcc through rational strain design. Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.

Xanthomonas is a phytopathogenic bacterium and of industrial interest due to its capability to produce xanthan, used as a thickener and emulsifier in the food and non-food industry. Until now, proteome analyses of Xcc lacking a detailed view on the proteins involved in xanthan biosynthesis. The proteins involved in the biosynthesis of this polysaccharide are located near, in or at the cell membrane. This study aims to establish a robust and rapid protocol for a comprehensive proteome analysis of Xcc strains, without the need to isolate different cell fractions. Therefore, a method for the analysis of the whole cell proteome was compared to the isolation of specific fractions regarding the total number of identified proteins, the overlap, and the differences between the approaches. The whole cell proteome analysis with extended peptide separation methods resulted in more than 3254 identified proteins covering 73.1% of the whole proteome. The protocol was used to study xanthan production in a label-free quantification approach. Expression profiles of 8 Gum proteins were compared between the stationary and logarithmic growth phase. Differential expression levels within the operon structure indicate a complex regulatory mechanism for xanthan biosynthesis. Data are available via ProteomeXchange with identifier PXD027261. SIGNIFICANCE: Bacteria are metabolite factories with a wide variety of natural products. Thus, proteome analyses play a crucial role to understand the biological processes within a cell behind the biosynthesis of those metabolites. Proteins involved in the biosynthesis of secreted products are often organised on, in or around the membrane allowing metabolite channelling. Experiments targeting those biosynthesis pathways on protein level often require the analysis of multiple cell fractions like cytosolic, inner, and outer membrane. This is time consuming and demands different protocols. The protocol presented here is a rapid and robust solution to study biosynthetic pathways of biological or biotechnological interest in a single approach on protein level, where gene products are partitioned across multiple cell fractions. The use of a single method also simplifies the comparison of different experiments, for example, production vs. nonproduction conditions. Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.