{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T00:50:30Z","timestamp":1760057430987,"version":"build-2065373602"},"reference-count":123,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,2,10]],"date-time":"2025-02-10T00:00:00Z","timestamp":1739145600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Austrian Science Fund (FWF)","award":["P-34860","BioToP W1224"],"award-info":[{"award-number":["P-34860","BioToP W1224"]}]},{"name":"Doctoral Program on Biomolecular Technology of Proteins","award":["P-34860","BioToP W1224"],"award-info":[{"award-number":["P-34860","BioToP W1224"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteomes"],"abstract":"<jats:p>Background: Chinese hamster ovary (CHO) cells are extensively used in the pharmaceutical industry for producing complex proteins, primarily because of their ability to perform human-like post-translational modifications. However, the efficiency of high-quality protein production can vary significantly for monoclonal antibody-producing cell lines, within the CHO host cell lines or by extrinsic factors. Methods: To investigate the complex cellular mechanisms underlying this variability, a phosphoproteomics analysis was performed using label-free quantitative liquid chromatography after a phosphopeptide enrichment of recombinant CHO cells producing two different antibodies and a tunicamycin treatment experiment. Using MaxQuant and Perseus for data analysis, we identified 2109 proteins and quantified 4059 phosphosites. Results: Significant phosphorylation dynamics were observed in nuclear proteins of cells producing the difficult-to-produce 2G12 mAb. It suggests that the expression of 2G12 regulates nuclear pathways based on increases and decreases in phosphorylation abundance. Furthermore, a substantial number of changes in the phosphorylation pattern related to tunicamycin treatment have been detected. TM treatment affects, among other phosphoproteins, the eukaryotic elongation factor 2 kinase (Eef2k). Conclusions: The alterations in the phosphorylation landscape of key proteins involved in cellular processes highlight the mechanisms behind stress-induced cellular responses.<\/jats:p>","DOI":"10.3390\/proteomes13010009","type":"journal-article","created":{"date-parts":[[2025,2,12]],"date-time":"2025-02-12T12:12:16Z","timestamp":1739362336000},"page":"9","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Systems Biology of Recombinant 2G12 and 353\/11 mAb Production in CHO-K1 Cell Lines at Phosphoproteome Level"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-9824-614X","authenticated-orcid":false,"given":"Eldi","family":"Sulaj","sequence":"first","affiliation":[{"name":"Department of Biotechnology and Food Science, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Felix L.","family":"Sandell","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Food Science, Institute of Computational Biology (ICB), BOKU University, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linda","family":"Schwaigerlehner","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Food Science, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1315-811X","authenticated-orcid":false,"given":"Gorji","family":"Marzban","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Food Science, Institute of Bioprocess Science and Engineering (IBSE), BOKU University, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juliane C.","family":"Dohm","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Food Science, Institute of Computational Biology (ICB), BOKU University, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3397-3621","authenticated-orcid":false,"given":"Renate","family":"Kunert","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Food Science, Institute of Animal Cell Technology and Systems Biology (IACTSB), BOKU University, Muthgasse 18, 1190 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1038\/s41587-022-01582-x","article-title":"Biopharmaceutical benchmarks 2022","volume":"40","author":"Walsh","year":"2022","journal-title":"Nat. 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