Genotoxicity Integration into Bioprocess Optimization Reveals Progressive DNA Damage During Bioreactor Expansion of Adipose-Derived Stem Cells

Mesenchymal stromal cells derived from adipose tissue (ASCs) are widely used in regenerative medicine, requiring scalable expansion strategies that preserve both cellular function and biological quality. However, current bioprocess optimization approaches are primarily guided by proliferation and phenotypic stability, often overlooking genomic integrity as a critical attribute. In this study, we developed a stirred-tank bioreactor system for ASC expansion on microcarriers and applied a genotoxicity-informed optimization strategy by integrating growth kinetics, metabolic profiling, and DNA damage assessment across multiple operational conditions (B1–B5), including variations in dissolved oxygen, agitation, inoculum density, and medium renewal. Optimized culture conditions (B5) enabled high cell productivity within a reduced cultivation period (9 days), while maintaining high viability (>90%), mesenchymal immunophenotype, and differentiation capacity. Distinct metabolic profiles were associated with enhanced proliferation, with increased glycolytic activity observed under optimized conditions. Despite these favorable outcomes, genotoxic analyses revealed a progressive, time-dependent accumulation of DNA damage and increased micronucleus frequency during expansion. Notably, these alterations did not impair cell proliferation, phenotype, or differentiation potential, indicating that conventional optimization metrics may not fully capture underlying genomic changes. Collectively, our findings demonstrate that bioprocess optimization based solely on classical performance parameters may overlook relevant biological alterations. By incorporating genotoxic endpoints into the evaluation framework, this study provides a refined approach for assessing large-scale stem cell expansion and contributes to improving the robustness and reliability of biomanufacturing strategies for therapeutic applications.