Comprehesive Rna-Sequencing Pipeline Of Cancer Xenograft Models

Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PASince a solid pipeline for massively parallel sequencing in cancer xenograft model has not been built yet, it is necessary to establish a precise analysis pipeline. Massively parallel sequencing on xenograft samples result in mixed sequencing reads from the engrafted human tumor cells and murine tissue. It is necessary to accurately distinguish between these reads for subsequent data analysis. In the present study, we constructed an integrated RNA-Seq pipeline including genomic variation, expression profiling, and fusion gene analysis. To distinguish these reads into individual species, we used the merged reference that incorporates the two genome reference from human (hg19) and mouse (mm10). We tested our pipeline using 6 Primary and 4 metastatic gastric tumor of 6 patients and their derivative xenografts sequencing data. There were almost same amount of ambiguous reads when we aligned sequencing reads to merged reference or separate reference genome. Using merged reference, we efficiently distinguished compound sequencing reads between human and mouse without repetitive alignment processes. The proportion of sequencing reads from mouse in xenograft samples widely ranged from 2.64% to 49.25% per each sample. For expression profiling, we used HTSeq-count for measuring expression level of each sample. As expected, human-specific reads of ECM-receptor and focal adhesion related genes were specifically down-regulated in the xenograft tumors compared to primary tumor and normal tissues suggesting the depletion of human cells from the microenvironment of engrafted tumor tissues. Mouse-specific reads of those genes were highly expressed in the engrafted tissue. Differentially expressed genes between engraft tumor and paired normal tissue were shown to be enriched in the cell cycle and p53 signaling pathway and these showed that engrafted tumor tissues well represent characteristics of cancer cells.Note: This abstract was not presented at the meeting.Citation Format: Jinha Hwang, Jong-Il Kim, Jee-Soo Choi, Min Jung Kim, Charles Lee. Comprehesive RNA-sequencing pipeline of cancer xenograft models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1938. doi:10.1158/1538-7445.AM2015-1938