Genomic analysis of drug resistant pancreatic cancer cell line by combining long non-coding RNA and mRNA expression profling.

Recently, more and more studies show that long non-coding RNAs (lncRNAs) play a very important role in various biological processes. However, research on lncRNA in the tumor cell drug resistance of it is seldom reported. In this study, gemcitabine-resistant pancreatic cancer cell line SWl990/GZ was obtained by treating parental cell line SWl990 in vitro with increasing dosage of gemcitabine in culture medium intermittently for ten months. We identified 4983 of 13310 detected lncRNAs demonstrated > 2-fold abnormally expressed in response to the gemcitabine-resistant, among of them, 1993 and 2990 lncRNAs were upregulated and downregulated. Meanwhile, 4759 mRNAs exhibited at least a 2-fold, of these, 2671 and 2088 mRNAs were upregulated and downregulated. Gene Ontology analysis and Pathway analysis revealed that differential expression mRNA involved in significant biological regulatory function and some genes may be particular to pancreatic cancer chemotherapy resistance. Quantitative real time PCR confirmed the changes of six lncRNAs (RP11-58D2.1, lincRNA-ZNF532, AP000221.1, CTC-338M12.5, CR619813, DDX6P) and nine mRNAs (SYT1, FAM171B, ZNF331, FAM187B, CYP1A1, SRXN1, HIST1H2BL, TOMM40L and SPP1) in SW1990 and SW1990/GZ. We also found that the upregulating of gemcitabine on the expression of lincRNA-ZNF532 was time-dependent. Gemcitabine at a range from 1.0 μM to 16.0 μM induced a increase of lincRNA-ZNF532 in SW1990 cells. The relative level of DDX6P is opposite to that of lincRNA-ZNF53 in the same circumstance. In conclusion, the dysregulated lncRNAs and mRNAs identified in this work may represent good candidates for future diagnostic or prognostic biomarkers and therapeutic targets.