Characterization of the ALDH1B1-dependent transcriptome in SW480 cells by RNA-seq

The mitochondrial enzyme ALDH1B1 is upregulated in colorectal and pancreatic adenocarcinomas and promotes tumor growth. Using both genetic and chemical perturbations, we have characterized the ALDH1B1-regulated transcriptome in a colorectal cancer cell line. Genes induced by ALDH1B1 include those related to mitochondrial metabolism, stemness, and ribosomal function. These findings implicate ALDH1B1 in cancer metabolism and cancer stem cell maintenance, and they underscore the potential of ALDH1B1 as a therapeutic target. Four experimental conditions were analyzed, each with three biological replicates. In all conditions, SW480 cells were cultured in RPMI-1640 medium containing 10% FBS and 100 U/mL penicillin-streptomycin. The first two conditions compared an ALDH1B1 knockout SW480 clone expressing EGFP and the same clone expressing ALDH1B1. The other two conditions compared the parental SW480 line treated with either DMSO or an ALDH1B1-selective inhibitor for 24 hours.