Bladder Cancer Response to Therapy Revealed by Whole Exome Sequencing

    Scientists at the University of Colorado Cancer Center say they used next-generation sequencing technologies to perform the most detailed DNA-based analysis to date of 25 commonly used bladder cancer cell lines. The work allowed the team to match patient tumors with their closest genetic cell line match and demonstrated genetic alterations that may make cells more or less sensitive to common therapies.

    “The idea is very simple but very important,” says Dan Theodorescu, M.D., Ph.D., director of the University of Colorado Cancer Center. “With our sequencing and transcriptional data, we can figure out which of these cell lines most closely match the human tumors. Once we know which ones match, we should only use these in our experiments in order to have the best chance that our experimental findings then apply to patients and their tumors.”

    Specifically, the study (“Molecular Analysis of Urothelial Cancer Cell Lines for Modeling Tumor Biology and Drug Response”), published in Oncogene, described the application of whole-exome sequencing to characterize genetic alterations that occur at the single-nucleotide level for all genes in 25 cell lines commonly used as models of bladder cancer. In combination with a separate technique that measures the degree to which a gene is expressed, the researchers then identified genes that were either mutated or functionally altered through expression levels in these bladder cancer cell lines.

    In all, the study found and validated 76 alterations in cancer-associated genes in the cell lines, many of which are involved in activating known oncogenes, including TERT, TP53, and PIK3CA. Importantly, this information can then be used to compare genetic aberrations in cell lines to human tumor samples.

    However, not all 76 genes were altered in all 25 cell lines, resulting in “signatures” of genetic changes that differed between lines. Like these cell lines, not all human bladder cancers share the same genetic changes. When the researchers compared these cell lines to the data of human tumors stored in The Cancer Genome Atlas (TCGA), they found that some cells lines better modeled some human tumors.

    “Instead of saying these cells look like oranges and these patients look like oranges, so they must be similar, this is an experiment to functionally show how similar or dissimilar these human tumors are to these cell lines at a molecular level,” explained Dr. Theodorescu.

    Along with differences in gene alterations, bladder cancer patients also show differences in how well they respond to certain therapies. In this case, researchers wondered whether the signatures that describe the genetic alterations in these 25 cell lines could predict the outcomes of patients treated with the common bladder cancer chemotherapy cisplatin.

    “In other words, we wanted to make sure these signatures were meaningful in real, human tumors and not just an artifact of being grown in a dish,” noted James Costello, Ph.D., investigator at the University of Colorado Cancer Center and assistant professor in the Univeristy of Colorado School of Medicine’s department of pharmacology.

    It turned out that, based on comparing the alterations found in these 25 cell lines with alterations found in a patient’s tumor, the researchers could predict who responded favorably and who did not respond to cisplatin treatment.

    “We don’t propose this as a current diagnostic or prognostic tool,” added Dr. Costello, “but showing that these alterations have real effect in human tumors allows us to explore the mechanisms that tumors use to resist therapies like cisplatin.”

    “Philosophically, we wanted to provide the bladder cancer field an atlas of cells that mirror human tumors so our collective experiments could be most relevant to patients. The study also adds to our understanding of disease development and therapy resistance,” pointed out Dr. Theodorescu.