Gene Expression Profiling Provides Insights into the Moleculor Mechanism of FGFR2+ Fibrocyte-to-Cancer Associated Fibroblast Differentiation in Esophageal Squamous Cell Carcinoma

To obtain an accurate overview of changes occurring during fibrocyte-to-cancer associated fibroblast differentiation in human esophageal squamous cell carcinoma (ESCC), we isolated circulating FGFR2+ fibrocytes and their paired FGFR2+ cancer associated fibroblasts (CAFs) from ESCC patients and compared their gene expression profiles by high-throughput RNA Sequencing. On average, about 55.08 million reads were obtained after eliminating low quality reads and 52.76 million reads (95.79%) were aligned to the human mRNA reference sequences. Transcripts corresponding to a total of 1,016 and 409 genes were found to be upregulated or downregulated at least two-fold in the combined set of two CAF sample pools, respectively. Furthermore, we identified the potential master regulators of CAF-specific extracelluar factors by motif enrichment analysis and addressed the molecular mechanisms underlying CAF differentiation. Whole transcriptome profiles of ESCC-derived FGFR2+ fibrocytes and CAFs were generated by deep sequencing using Illumina GAIIx. FGFR2+ fibrocytes were isolated from blood samples of 9 ESCC patients, while, FGFR2+ CAFs were isolated from marched ESCC tissues. Sample pooling strategy was employed to reduce the effects of individual variation. Samples (total RNA) were pooled into two groups: group 1 combined 5 samples of fibrocytes (Fbc-1) and corresponding paired CAFs (CAF-1), while group 2 combined 4 samples of fibrocytes (Fbc-2) and marched CAFs (CAF-2).