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Tobacco use disorder is frequently comorbid with emotional disorders, each exerting reciprocal influence on the other. As an important hub for emotional processing, amygdala may also play a critical role in tobacco addiction. Therefore, we aimed to investigate the volume and spontaneous activity of the amygdala in nicotine-dependent individuals and their relationships with cigarette use. A total of 84 smokers (aged 22–54 years) and 41 nonsmokers (aged 26–56 years) were enrolled in the present study. 3D-T1 weighted images and resting-state fMRI images were acquired from all participants. We used ROI-wise volume, fractional amplitude of low frequency fluctuation (fALFF) and resting-state functional connectivity (FC) to assess structural and functional changes of the amygdala in the smokers. There was no significant difference between smokers and nonsmokers on amygdala volume (p > 0.05). When compared to nonsmokers, increased fALFF in the right amygdala was observed in smokers (p = 0.024). In addition, increased FC between the left amygdala and the right precuneus and decreased FC between the right amygdala and the right orbitofrontal cortex (OFC) was found in smokers. In smokers, these amygdala measures did not correlate with any measures of cigarette use. The results revealed that the amygdala function but not volume was affected in nicotine addiction. When considering the fALFF and FC results, we propose that the OFC top-down control may regulate the amygdala activity in nicotine addicts. The pattern of amygdala-based FC in smokers revealed in our study may provide new information about the brain circuitry of tobacco dependence.Amygdala volume and function were compared between smokers and nonsmokers.Different patterns of amygdala-based functional connectivity (FC) in smokers.Reduced amygdala-OFC FC top-down control induced high fALFF in amygdala in smokers.