DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase-9 inhibition in chondrogenic cells

0572630 - ÚŽFG 2024 RIV US eng J - Článek v odborném periodiku
Lapcik, P. - Veselá, Barbora - Potěšil, D. - Dadáková, Kateřina - Zapletalová, Martina - Beneš, P. - Bouchal, P. - Matalová, Eva
DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase-9 inhibition in chondrogenic cells.
Proteomics. Roč. 23, č. 11 (2023), č. článku 2200408. ISSN 1615-9853. E-ISSN 1615-9861
Grant CEP: GA ČR(CZ) GA19-14727S; GA MŠMT LM2023042
Institucionální podpora: RVO:67985904
Klíčová slova: caspase-9 * chondrogenesis * diaPASEF * micromass cultures * proteomics
Obor OECD: Cell biology
Impakt faktor: 3.4, rok: 2022
Způsob publikování: Open access
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200408

Caspase-9 is the major apical caspase responsible for triggering the intrinsic apoptotic pathway. Our previous study indicated that specific inhibition of caspase-9 caused microscopically evident alterations in appearance of the primary chondrogenic cultures which cannot be explained by decrease in apoptosis. To describe a complex molecular background of this effect, proteomics analysis of control and caspase-9 inhibitor-treated chondrogenic cultures were performed. Proteins were extracted, identified and quantified using LC-MS in both data dependent and data independent acquisition (DIA) mode. While directDIA analysis of diaPASEF data obtained using timsTOF Pro LC-MS system revealed 7849 protein groups (Q-value <0.01), a parallel analysis of iTRAQ-2DLC-MS3 and conventional DIA-MS data identified only 5146 and 4098 protein groups, respectively, showing diaPASEF a superior method for the study. The detailed analysis of diaPASEF data disclosed 236/551 significantly down-/up-regulated protein groups after caspase-9 inhibition, respectively (|log2FC|>0.58, Q value <0.05). Classification of downregulated proteins revealed changes in extracellular matrix organization, collagen metabolism, and muscle system processes. Moreover, deregulations suggest a switch from glycolytic to lipid based metabolism in the inhibited cells. No essential changes were found in the proteins involved in apoptosis. The data indicate new non-apoptotic participation of caspases in chondrocyte homeostasis with potential applications in cartilage pathophysiology.
Trvalý link: https://hdl.handle.net/11104/0343686