Wnt signaling inhibition in human colon cancer cell lines (SW480 and SW620) drives changes in gene programs for cell adhesion, mobility, and cell junction

Overactive Wnt signaling has been found to be a significant driver in colon cancer carcinogenesis targeting many cellular processes such as cel proliferation, migration, and metabolism. The purpose of this study was to use high throughput transcriptional profiling (RNA-seq) to identify Wnt signaling gene targets in human colon cancer cells. Transcriptional profiles of human colon cancer cell lines (SW480 and SW620) with overactive Wnt signaling were compared to their matching Wnt low genetically modified stable cell (SW480-dnLEF1 and SW620-dnLEF1) through high throughput RNA-seq with four biological replicates. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat2 followed by HTseq and DESEQ2. Using an optimized data analysis workflow, we mapped about 30-40 million sequence reads per sample to the human genome (build hg38). RNAseq analysis of dnLEF1 expression in SW480 and SW620 cells cultured in vitro showed changes in gene programs for cell adhesion, mobility, cell junction, and extracellular matrix. Overall design: Experiment 1: SW480 GFP (mock/control) vs SW480 dnLEF1 (Wnt inhibited/experimental) Experiment 2: SW620 GFP (mock/control) vs SW620 dnLEF1 (Wnt inhibited/experimental)