Ancient Trypsinogen Duplications Shape Pancreatic Disease Risk through Pseudogene Enhancers

Understanding how ancient gene duplications influence contemporary disease remains a central challenge in evolutionary medicine. Here we show that primate-specific duplications at the trypsinogen (PRSS1/PRSS2) locus have shaped human pancreatic disease susceptibility through retained regulatory functions of pseudogenes. Comparative genomic analyses reveal tandem duplications arising during the Oligocene (~24–34 million years ago), followed by human-specific copy loss that generated two major haplotypes: an ancestral 5-copy form prevalent in African populations and a derived 3-copy form that rose to high frequency outside Africa. Notably, the frequency of the derived, protective haplotype is tightly correlated with copy number expansion of amylase genes, linking adaptation to starch-rich diets with moderated trypsin output. Although the pseudogenized copies (PRSS3P2 and TRY7) no longer encode proteins, epigenomic profiling, allelic expression analyses and dual-luciferase reporter assays demonstrate that they retain pancreas-specific enhancer activity, increasing PRSS2 expression by ~15–30% in 5-copy carriers relative to 3-copy individuals. Consistent with this functional divergence, East Asian populations exhibit strong signatures of positive selection on the 3-copy haplotype (dN/dS > 1; P < 0.05), accompanied by reduced pancreatitis risk (OR = 1.79 for the 5-copy haplotype). Together, these findings establish a paradigm in which ancient gene duplications influence present-day disease risk through regulatory functions preserved in pseudogenes, highlighting diet-driven evolutionary trade-offs in human pancreatic biology.