Functional connectivity changes in the thalamocortical network due to neck pain and the multiscale regulatory effects of acupuncture: a cross-scale multi-omics neuroimaging study

Background Neck pain correlates with multiscale brain abnormalities, but cross-scale mechanisms of acupuncture analgesia are unclear. This study aimed to: (1) Explore differential modulation of thalamic functional networks by verum vs. sham acupuncture; (2) Examine associations between functional connectivity changes and micro gene expression to unravel its multiscale mechanisms. Methods A total of 130 participants were initially enrolled, and 100 eligible neck pain patients were randomized 1:1 to the verum ( n = 50) or sham ( n = 50) acupuncture groups. Finally, 49 patients in each group were included for the final analysis due to one case of exclusion in each group, with treatment administered twice a week for 2 weeks. Visual Analog Scale (VAS), resting-state functional magnetic resonance imaging (fMRI), and Allen Human Brain Atlas (AHBA) transcriptome data were analyzed via Partial Least Squares (PLS) regression. Results Both groups showed reduced post-treatment VAS ( p < 0.001), with the verum group exhibiting a superior effect ( Z = −6.877, p < 0.001). Neuroimaging revealed that verum acupuncture (VA) specifically induced significant decreases in functional connectivity (FC) between the right thalamus and left anterior cingulate cortex ( T = −4.498) as well as between the right thalamus and right Rolandic operculum ( T = −4.532, voxel-level p < 0.01, cluster-level p < 0.05), an effect absent in the sham acupuncture group (SA). Gene- FC association analysis indicated that PLS2 component explained 39.83% of FC variance ( P spin : permutation test p < 0.05), with weight genes showing significant spatial correlation to connectivity changes ( r = 0.445, P spin = 0.0011). A total of 809 genes were enriched in the innate immune response and phosphorylation regulation pathways, whereas 1,222 genes were enriched in the GABA-ergic synapse and synaptic membrane-related pathways. Conclusion VA relieves pain via modulating thalamus-anterior cingulate cortex networks, involving immune-inflammation and neural inhibition, providing first multi-scale validation integrating neuroimaging and transcriptomics. Clinical trial registration This trial was registered with the International Traditional Medicine Clinical Trial Registry (registration number: ITMCTR2023000001) prior to participant enrollment.