ObjectiveTo investigate the expression of Midkine （MDK） in cholangiocarcinoma （CCA） and its value in predicting the prognosis of CCA， as well as the potential mechanism of the effect of MDK on the progression of CCA. MethodsThe data of CCA samples were obtained from TCGA database to analyze the difference in the expression of MDK between cancer tissue and paracancerous tissue and its association with clinical features， and the data collected from GEO database and 11 CCA patients who underwent surgical resection in The Fifth Medical Center of Chinese PLA General Hospital from June 2018 to September 2021 were used for validation. STRING and Cytoscape were used to construct a protein-protein interaction network， and gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analyses were used to investigate the biological functions and tumor-related pathways involving MDK-related genes. In addition， TIMER and TISIDB databases were used to analyze the correlation between MDK expression and immune cell infiltration in CCA tissue. The independent-samples t test or the Mann-Whitney U test was used for comparison of continuous data between two groups， and the Fisher’s exact test was used for comparison of categorical data between two groups. The Kaplan-Meier method was used to plot survival curves， and the Log-rank test was used for comparison between groups. The Spearman correlation analysis was used to investigate the correlation between two variables. ResultsThe expression level of MDK in cancer tissue and paracancerous tissue of CCA patients was compared based on TCGA database， and the results of the non-paired and paired analyses showed that the expression level of MDK in CCA tumor tissue was significantly higher than that in paracancerous tissue （P<0.001）. Transcriptome sequencing was performed for the tumor tissue and its corresponding paracancerous tissue from 11 CCA patients， and the results showed that the expression level of MDK in CCA tumor tissue was significantly higher than that in corresponding paracancerous tissue （P<0.01）. High expression of MDK was associated with lymph node metastasis （P=0.045） and vascular invasion （P=0.044）. Survival analysis showed that compared with the CCA patients with low MDK expression， the CCA patients with high MDK expression had significantly shorter overall survival time （χ²=5.30， P=0.028） and disease-specific survival time （χ²=6.25， P=0.019）. The GO and KEGG enrichment analyses showed that the 30 MDK-related genes were closely associated with ubiquitin-mediated proteolysis and affected the prognosis of CCA patients. The TIMER analysis showed that the expression level of MDK was positively correlated with the infiltration of B cells （r=0.356， P=0.035 6） and dendritic cells （r=0.409， P=0.014 7） in tumor microenvironment of CCA； the TISIDB analysis showed that the expression level of MDK was positively correlated with CXCL16 （r=0.465， P=0.004 67） and was negatively correlated with CXCL12 （r=-0.389， P=0.019 7） and CXCR5 （r=-0.393， P=0.018 5）， and it was also negatively correlated with the immune checkpoint regulators VTCN1 （r=-0.393， P=0.018 3）， LTA （r=-0.380， P=0.022 7）， and PVR （r=-0.350， P=0.037 3）. ConclusionHigh expression of MDK is associated with poor prognosis in CCA patients， and MDK has the potential of being used as a molecular marker for predicting the prognosis of CCA. MDK may promote the development and progression of CCA by regulating ubiquitin-mediated proteolysis and the infiltration of B cells and dendritic cells.