Structural evolution of trypsinogen gene redundancy confers risk for pancreas diseases

Trypsin is an important enzyme secreted by the pancreas for digesting proteins. The precursors of major human trypsin are encoded by trypsinogen genes PRSS1 and PRSS2 . Here, we leveraged multi-omic data to study their evolutionary and functional impact. We estimated that the primate trypsinogen gene was duplicated from a single copy to multiple-copy 24-34 million years ago (Mya). Compared to six protein-coding genes in non-human great apes, the human ancestral state was a 5-copy with three being pseudogenized. Interestingly, a derived 3-copy form emerged in Africans ∼260 Kya and dominated in non-Africans as one of the two major haplotypes. Although no longer encoding proteins, the pseudogene enhancers still function on pancreatic PRSS2 expression, leading to ∼15% up-regulation for the 5-copy than the 3-copy haplotype. Notably, the 3-copy structure was under positive selection in East Asians, where lower trypsin might be adaptive during high-starch diet shift for protecting the pancreas from autodigestion, as also supported by the identified causality of the haplotype structure to pancreatitis risk. Our efforts in elucidating the structural evolution of trypsinogen genes advance our understanding of the genetic basis and molecular mechanism of human pancreas diseases. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was supported by the National Natural Science Foundation of China (NSFC) grant (32030020, 31871256, and 31961130380), the Strategic Priority Research Program (XDPB17, XDB38000000) of the Chinese Academy of Sciences (CAS), the UK Royal Society-Newton Advanced Fellowship (NAF\R1\191094), and the Shanghai Municipal Science and Technology Major Project (2017SHZDZX01). The funders had no role in the study design, data collection, analysis, decision to publish, or preparation of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study used ONLY openly available human data that were originally located at NCBI, ENCODE project, 1000 Genomes Project, Human Genome Diversity Project, SEER and GTEx project. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data are publicly available online, see 'Data Availability' section in the manuscript for accession numbers.