Background: Treatment of acute pancreatitis (AP) and chronic pancreatitis (CP) remains problematic due to a lack of knowledge about disease-specific regulatory targets and mechanisms. The purpose of this study was to screen proteins related to endoplasmic reticulum (ER) stress and apoptosis pathways that may play a role in pancreatitis. Methods: Human pancreatic tissues including AP, CP and healthy volunteers were collected during surgery. Humanized PRSS1 transgenic mice were constructed and treated with caerulein to mimic the development of human AP and CP. Potential regulatory proteins in pancreatitis were identified by proteomic screen using pancreatic tissues of PRSS1 transgenic AP mice. Adenoviral shRNA-mediated knockdown of identified proteins, followed by functional assays was performed to validate their roles. Functional analyses included transmission electron microscopy for ultrastructural analysis; qPCR, western blotting, immunohistochemistry, immunofluorescence and immunoelectron microscopy for assessment of gene or protein expression, and TUNEL assays for assessment of acinar cell apoptosis. Findings: Humanized PRSS1 transgenic mice could mimic the development of human pancreatic inflammatory diseases. EMC6 and APAF1 were identified as potential regulatory molecules in AP and CP models by proteomic analysis. 1) increased expression of EMC6 and APAF1 was observed in patient and mouse AP/CP tissues; 2) inhibition of the two proteins resulted in attenuation of apoptosis and inflammation; 3) inhibition of EMC6 was associated with decreased expression of APAF1, suggesting a potential mechanistic connectivity. Interpretation: EMC6 and APAF1 are strongly associated with pancreatitis development, and may represent therapeutic targets for the treatment of pancreatic inflammatory diseases. Funding Statement: The article is supported by Guangdong Science and Technology Planning Project (2019A030317018) & Scientific Research Startup Program of Southern Medical University by High-level University Construction Funding of Guangdong Provincial Department of Education (CX2018N012) & Clinical Research Program of Nanfang Hospital, Southern Medical University (2018CR046) & College Students’ Innovative Entrepreneurial Training Plan Program (201812121128, 201812121263) & Clinical Research Startup Program of Southern Medical University by High-level University Construction Funding of Guangdong Provincial Department of Education (LC2016PY011) & National Natural Science Foundation of China (81801487). Declaration of Interests: The authors declare no conflict of interest. Ethics Approval Statement: Written consent was obtained from each patient before the study, which were approved by the Ethics Committee of the Southern Medical University. The experimental operations were carried out in strict accordance with the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health and were approved by the Institutional Animal Care and Use Committee of Southern Medical University.