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(1) This study compared [⁶⁸Ga]PentixaFor uptake in active arterial segments with corresponding [¹⁸F]FDG arterial uptake as well as the relationship with cardiac [⁶⁸Ga]PentixaFor uptake. (2) Method: Tracer uptake on atherosclerotic lesions in the large arteries was measured and target-to-background ratios (TBR) were calculated to adjust background signals with two investigators blinded to the other PET scan. On a patient-based and lesion-to-lesion analysis, TBR values of two tracers were compared and the relationship with cardiac inflammation was further explored. Furthermore, two cardiovascular risk-related groups were divided to explore the value of risk stratification of the two tracers in atherosclerosis. (3) Results: [⁶⁸Ga]PentixaFor PET/MRI identified more lesions (88% vs. 48%; <i>p</i> < 0.001) and showed higher uptake than [¹⁸F]FDG PET/MRI (TBR, 1.90 ± 0.36 vs. 1.63 ± 0.29; <i>p</i> < 0.001). In the patient-based analysis, the TBR of [⁶⁸Ga]PentixaFor uptake was also significantly higher than [¹⁸F]FDG uptake (1.85 ± 0.20 vs. 1.42 ± 0.19; <i>p</i> < 0.001). The TBR of active lesions for [⁶⁸Ga]PentixaFor was significantly increased in the high-risk group (<i>n</i> = 9), as compared to the low-risk group (<i>n</i> = 10) (2.02 ± 0.15 vs. 1.86 ± 0.10, <i>p</i> = 0.015), but not for [¹⁸F]FDG (1.85 ± 0.10 vs. 1.80 ± 0.07, <i>p</i> = 0.149). (4) Conclusion: [⁶⁸Ga]PentixaFor PET/MRI identified many more lesions than [¹⁸F]FDG PET/MRI. Patients with high-risk cardiovascular factors illustrated an increased uptake of [⁶⁸Ga]PentixaFor. There was a correlation between the elevated uptake of [⁶⁸Ga]PentixaFor in the active arterial segments and heart.