Abstract 1535: Next generation sequencing of brain metastasis in non-small cell lung cancer
Authors: Thibodeau Bryan , Yumpo Cardenas Paola , Ahmed Samreen , Dunn Marc , Johnson Matthew , Wilson George 
Published: July 2016

Abstract
Introduction: Molecular analysis of non-small cell lung cancer (NSCLC) has provided a detailed classification of NSCLC. Activating mutations in the EGFR gene are both prognostic and predictive in that they are associated with improved survival irrespective of therapy and are associated with a significant response to EGFR tyrosine kinase inhibitors (TKIs) such as gefitinib or erlotinib. Patients with EGFR mutations show a significant improvement in progression free survival compared to standard chemotherapy. In addition, a recent study showed that ALK gene rearrangement was significantly associated with pericardial spread and pleural disease and those patients with either ALK gene rearrangements or EGFR mutations were predisposed to liver metastasis. These results support the hypothesis that the dominant molecular oncogenes in NSCLC are associated with different biological behaviors which manifest as distinct patterns of metastatic spread at the time of diagnosis. To date, no pattern of molecular variation has been linked to brain metastasis. Here we use next generation sequencing to identify a pattern of genomic variation associated with the development of brain metastases in NSCLC. Methods: Three patient groups were analyzed: samples from NSCLC patients who did not develop metastasis (n = 8), samples from NSCLC patients who developed metastasis not associated with the central nervous system (n = 7), and brain metastasis samples of NSCLC patients (n = 16). DNA was isolated, and libraries prepared using Qiagen's Comprehensive Cancer Panel which focuses on 160 cancer-related genes. Libraries were sequenced on the Illumina NextSeq 500. Alignment was done using SoftGenetic's NextGENe with subsequent biological interpretation with Ingenuity Variant Analysis. Results: At the variant level, a missense mutation in CDK12 (chr1:37686934) was found in 7 of the 16 cases with brain metastasis while only 1 of 8 cases with no metastasis and 0 of 7 cases with non-CNS metastasis had the variant. However, no other variants were found in ≥6 cases of brain metastasis and 1 or less of the control cases. After filtering variants that occurred in more than 1 control (no metastasis or non-CNS metastasis), the TP53 gene was altered in 11 of the 16 cases with brain metastasis. This included 14 different variants with none of these variants present in the controls. Additionally, BRCA1 and CDK12 had variants in 9 cases with brain metastasis, but the variant was also present in 1 of the controls. Taken together, all 16 cases contained alterations in at least 1 gene involved in PI3K/AKT signaling including variants in JAK1, MTOR, TP53, TSC1, and TSC2. Conclusion: This pilot study has delivered valuable results to better characterize the pattern of genomic variants in NSCLC. While no single variant was associated with brain metastasis, this study implicates PI3K/AKT signaling and, in particular, variants of TP53 as crucial for determining the potential development of NSCLC brain metastasis.
Citation Format: Bryan Thibodeau, Paola Yumpo Cardenas, Samreen Ahmed, Marc Dunn, Matthew Johnson, George Wilson. Next generation sequencing of brain metastasis in non-small cell lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1535.