Whole exome sequencing of DNA from cancer cells exposed to chronic hypoxia and normoxia

Hypoxia is a condition that commonly occurs in the microenvironment of solid tumors and has been associated with genomic instability. In this study, whole exome sequencing analysis was conducted to determine the effect of chronic, long passaging, at 1% oxygen (hypoxia) on genomic instability in cancer cells. The cancer cell lines included were two pancreatic (MIA PaCa-2, Capan-1), one lung (H226), one breast (MCF-7), one colon (HT-29), and one ovarian (SKOV-3). They were selected from a panel of 12 cancer cell lines ranked according to their sensitivity to hypoxia based on an 8-gene hypoxia signature. H226, MCF-7 and HT-29 showed the highest sensitivity and were characterized as hypoxia high (HH) and MIA PaCa-2, Capan-1 and SKOV-3 showed the lowest sensitivity and were characterized as hypoxia low (HL). DNA samples collected from chronic hypoxia and from normoxia of each cell line were exposed to whole exome sequencing. Variations in tumor mutational burden and copy number alterations could then be reported in hypoxic cells.