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D..G. Bebb

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    MINI 35 - Biology (ID 161)

    • Event: WCLC 2015
    • Type: Mini Oral
    • Track: Biology, Pathology, and Molecular Testing
    • Presentations: 1
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      MINI35.07 - ATM Mutations in Cancer Cell Lines Predict Higher Mutation Rates and Genetic Instability (ID 1704)

      18:30 - 20:00  |  Author(s): D..G. Bebb

      • Abstract
      • Presentation
      • Slides

      Ataxia telangiectasia-mutated (ATM) is a critical first responder in the cell to DNA damage. Individuals lacking ATM are extremely sensitive to DNA-damaging ionizing radiation, and are predisposed to develop cancers. The mechanism for ATM dysfunction in A-T patients, or cancer patients that are ATM-deficient, is unknown. ATM has been sequenced in lung cancer patient samples, but no specific mutation hotspots have been linked with disease development, despite ATM being one of the most mutated genes in lung cancer. Our own quantitative analysis of ATM protein levels in patient samples suggests that expression is lost in 20-25% of cases and that this loss correlates with poor overall survival and increased response to adjuvant chemotherapy treatments. We believe that this may be the result of increased genomic instability within the cancer cells caused by a lack of adequate DNA repair. Given that ATM-deficient cancer cells may have higher genetic instability, and that ATM is so highly mutated in lung cancer, we sought to quantify the relationship between ATM mutations and genomic instability, as measured by total somatic mutations.

      Using data available from the Broad Institute’s Cancer Cell Line Encyclopedia (CCLE), we correlated mutations in ATM and other genes involved with the DNA repair response with the total number of mutations annotated in ~900 cancer cell lines. We also analyzed total mutations per cell line against the functional impact score of single nucleotide variations (SNVs) within ATM. To determine the clinical relevance of the cancer cell line observations, we partnered with the BC Genome Sciences Centre (BCGSC) to perform similar analyses on ~100 whole-genome-sequenced patient samples.

      We show that in cell lines across all cancer types, mutations in ATM correlate with a significantly higher number of total mutations. When analyzed by site of origin, the greatest differences in total mutations were found in lung, breast, intestinal, and esophageal cancer cells. We examined additional genes associated with the DNA-repair response, including direct response genes (i.e. ATR, BRCA1&2) and downstream targets (i.e. p53). Only mutations in the direct response genes appeared to associate with total mutations, whereas p53 – while more commonly mutated – did not correlate with higher mutations. In 10 lung cancer patients, one had a truncating mutation and had the second highest number of somatic mutations, and highest among non-smokers.

      We have identified a potential relationship between ATM mutation and total somatic mutations in cancer cell lines and patient tumour genomes, which may be indicative of overall genetic instability in these samples. Analysis of the ATM mutations in cell lines and patient samples clearly shows that there are no specific hotspots for mutation in ATM that correlate with increased total mutations. Thus screening for ATM mutations alone may not be sufficient to indicate loss of function or instability. However, this data may prove useful in developing panels of targets to screen as mutation hotspots of instability, and ultimately to help identify patients that may benefit from targeted or modified therapy options based on ATM-deficiency or higher genetic instability.

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