Transcriptomic comparison of human intestinal organoids and Caco-2 cells in modeling nutrient absorption: insights from infant formula and breast milk

Infant nutrition is crucial for early development, with breast milk regarded as the gold standard. However, replicating its nutrient absorption and metabolic outcomes in infant formula remains challenging. This study utilized transcriptomic analysis to compare human small intestinal organoids (SIOs) and Caco-2 cells as models for nutrient absorption across three types of infant formula and breast milk. RNA sequencing revealed that SIOs exhibited greater Euclidean distance distributions and achieved more precise hierarchical clustering compared to Caco-2 cells. Differential expression analysis identified a higher number of differentially expressed genes in SIOs, along with significant enrichment of growth and developmental pathways, including embryonic morphogenesis, providing a closer approximation of human intestinal processes. Moreover, our analysis demonstrated that breast milk exhibits unique metabolic signatures distinct from all infant formulas evaluated, reinforcing its established role as the nutritional gold standard. Subsequent toxicological assessment revealed elevated oxidative stress-related metabolites in formulas processed via two-step wet blending, suggesting potential long-term metabolic risks. These findings establish SIOs as a superior model for studying nutrient absorption and toxicological effects, emphasizing the need for optimized formula processing techniques and further clinical validation.