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Purpose: Many studies have shown that obesity is one of the major causes of lung function decline. However, a longitudinal study of the correlation between changes in obesity degree and lung function is still lacking. This study aimed to analyze alterations in lung function according to changes in body and abdominal fat amount over time in healthy individuals. Methods: A retrospective cohort study of individuals who received annual health screening was performed. Individuals who underwent health screening at least 3 times with follow-up periods more than 5 years were included. Using a linear mixed model, we analyzed associations between the change in total body fat amount/abdominal fat ratio and lung function decline over time by dividing each quartile according to the fat change rate. Results: A total of 15,484 individuals over 40 years old was enrolled prospectively. A longitudinal increase in total body fat amount over time was associated with a predicted value of forced expiratory volume in 1 second (FEV1p; %) and predicted value of forced vital capacity (FVCp; %) declines, regardless of sex. A similar phenomenon was observed between an increase in abdominal fat ratio and FEV1p/FVCp decline, which was predominant in males. In addition, the change in abdominal fat ratio showed a significant correlation with differences in the initial values of FEV1p and FVCp after 40 years old. Conclusion: Increases in total body fat amount and abdominal fat ratio may cause lung function decline over time.