A TRANSCRIPTOMICS APPROACH TO STUDYING THE HELICOBACTER PYLORI AND GASTRIC CANCER PARADIGM

Background: Gastric cancer is responsible for the second highest incidence of cancer-related deaths and is the fourth most common type of cancer. One of the main etiological factors attributing to gastric cancer is the presence of Helicobacter pylori. H. pylori is the only bacteria considered to be a carcinogen, due to its ability to promote carcinogenesis in gastric tissue. A previous study used next generation sequencing to identify H. pylori in gastric tumor and adjacent samples and determine differentially expressed genes in H. pylori and the host. We sought to further investigate differentially expressed genes by co-culturing H. pyloriwith gastric epithelial cells. Methods: N87 gastric epithelial cells were cultured with H. pylori 26695 and H. pylori 26695 without the cag pathogenicity island for 24 hours. RNA was extracted from the co-cultures at 2, 4, and 24 hours. RNA from N87 cells alone and from both H. pylori strains cultured in tissue culture media at 0, 2, 4 and 24 hours were used as controls. Human transcriptome libraries were poly-A selected, H. pylori control libraries were created from ribo-reduced total RNA, and H. pylori transcriptomes from co-culture were captured with a H. pylorispecific Agilent Sure Select kit. Transcriptome sequences were analyzed using in-house prokaryotic and eukaryotic RNASeq pipelines and differential expression analysis was conducted with edgeR. Results: Our analysis evaluated differentially expressed human and H. pylori genes for every possible comparison and across all of the samples. Genes encoded on the cag pathogenicity island were differentially expressed in most of the comparisons between co-culture samples with and without the pathogenicity island, as was expected. About 106 H. pylori genes were differentially expressed in at least one comparison. Analysis of host transcriptomics is ongoing. Based on previous results, we expect that human genes involved in regulation of stomach acidity, like gastrin and pepsinogen, will be differentially expressed. Conclusions: This study is the first in-depth transcriptomics analysis of H. pylori and human cells in co-culture. Pathogenic and protein synthesis genes were differentially expressed when comparing H. pylori strains in co-culture with and without the pathogenicity island. Overall, this work will enhance the knowledge of the importance of the pathogenicity island as it relates to the host response.