Chronic pain (CP) is a widespread and debilitating condition with complex neurobiological and genetic foundations. To better understand the brain-based and genetic mechanisms underlying CP, we integrated bidirectional Mendelian randomization (MR), local genetic correlation analysis (LAVA), and multi-trait colocalization (HyPrColoc) using data from 3935 brain imaging-derived phenotypes (IDPs). CP was characterized using three definitions: multisite chronic pain (MCP), chronic widespread pain (CWP), and general chronic pain (GCP). MR analyses highlighted several brain IDPs, cortical areas such as the anterior cingulate, superior frontal, and inferior frontal gyri, as having potential causal effects on CP risk. Additional findings pointed to the role of resting-state connectivity and cerebellar white matter microstructure. LAVA results indicated local genetic correlations between brain features and CP in regions involved in synaptic remodeling, immune-inflammatory activity, and neurodevelopment. Multi-trait colocalization pinpointed the shared variant - rs1873914, potentially linking CP, IDPs, and SUOX gene expression. Together, these findings suggest that some brain structures and their functions may play a causal role in the development of chronic pain.

This study integrates brain imaging phenotypes with genetic analyses to clarify causal links in chronic pain. By combining MR, LAVA, and HyPrColoc, we identify structural and functional brain features, pathways, and candidate genes that may underlie pain chronification, offering targets for mechanistic studies and interventions.