CXCL Gene Clusters Regulated by Enhancer-Mediated DNA Looping Alteration in Pancreatic Cancer Cells

Pancreatic cancer is one of the deadliest cancers. Chemokines affect the progression of pancreatic cancer through various mechanisms. Most of the CXC chemokine genes, CC chemokine genes and CX3C chemokine genes are clustered together within a very short region of chromatin. Transcription activity of gene clusters is usually influenced by the chromatin architecture and spatial organisation. Nevertheless, the chromatin-mediated regulatory mechanism on transcription of chemokine gene clusters has never been studied in pancreatic cancer. Herein, we determined that the expression of C-X-C motif chemokine ligand 8 (CXCL8), CXCL6, CXCL4L1, CXCL1, CXCL4, CXCL7, CXCL5, CXCL3 and CXCL2 was up-regulated, whereas CXCL9, CXCL10 and CXCL11 were down-regulated in pancreatic cancer cells compared with normal duct epithelial cells and further uncovered that four enhancer elements showed robust interaction to form DNA looping containing the up-regulated eight CXCL genes, whereas the other enhancer controlled CXCL9, CXCL10 and CXCL11 to form another DNA loop. Furthermore, after these enhancers were respectively destroyed by CRISPR-Cas9, we observed that the interaction with other enhancers was weakened as well as the expression of CXCL gene clusters and the tumour malignancy of pancreatic cancer cells was significantly changed. Taken together, our research exhibits the regulatory mechanism on transcription of CXCL gene clusters via enhance-dependent DNA looping alteration in pancreatic cancer cells.