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S. Ansén



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    ORAL 06 - Next Generation Sequencing and Testing Implications (ID 90)

    • Event: WCLC 2015
    • Type: Oral Session
    • Track: Biology, Pathology, and Molecular Testing
    • Presentations: 1
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      ORAL06.01 - Genomic Characterization of Large-Cell Neuroendocrine Lung Tumors (ID 1667)

      10:45 - 12:15  |  Author(s): S. Ansén

      • Abstract
      • Slides

      Background:
      Neuroendocrine lung tumours account for 25% of all lung cancer cases, and they range from low-aggressive pulmonary carcinoids (PCA) to highly malignant small-cell lung cancer (SCLC) and large-cell neuroendocrine lung carcinoma (LCNEC). The last two are strongly associated with heavy smoking and are typically detected at a clinically advanced stage, having a poor survival. Comprehensive genomic analyses in lung neuroendocrine tumours are difficult because of limited availability of tissue. While more effort has been done in the context of SCLC, the detailed molecular features of LCNEC remain largely unknown.

      Methods:
      We conducted 6.0 SNP array analyses of 60 LCNEC tumours, exome sequencing of 55 tumor-normal pairs, genome sequencing of 11 tumour-normal pairs, transcriptome sequencing of 69 tumours, and expression arrays on 60 tumors. Data analyses were performed using in house developed and published pipelines.

      Results:
      Analyses of chromosomal gene copy number revealed amplifications of MYCL1, FGFR1, MYC, IRS2 and TTF1. We also observed deletions of CDKN2A and PTPRD. TTF1 amplifications are characteristic of lung adenocarcinoma (AD); CDKN2A deletions are frequent alterations in both AD and squamous-cell lung carcinoma (SQ); FGFR1 amplifications are found in SQ and, less frequently, in SCLC; and MYCL1 and IRS2 amplifications are frequent events in SCLC. Similar to the copy number data, we found patterns of mutations characteristic of other lung cancer subtypes: TP53 was the most frequently mutated gene (75%) followed by RB1 (27%), and inactivation of both TP53 and RB1, which is the hallmark of SCLC, occurred in 20% of the cases. Mutations in STK11 and KEAP1-NFE2L2 (frequently seen in AD and SQ) were found in 23% and 22% of the specimens, respectively. Interestingly, mutations in RB1 and STK11/KEAP1 occurred in a mutually exclusive fashion (p-value=0.016). Despite the heterogeneity observed at the mutation level, analysis of the pattern of expression of LCNEC in comparison with the other lung cancer subtypes (AD, SQ, SCLC, and PCA) points to LCNEC as being an independent entity. An average mutation rate of 10.7 mutations per megabase was detected in LCNEC, which is in line with the rate observed in other lung tumours associated with smoking. We found that, similar to SCLC, the mutation signatures associated with APOBEC family of cytidine deaminases, smoking, and age (based on Alexandrov et al 2013) were the predominant ones in LCNEC. However, the contribution of the individual SCLC and LCNEC samples to these three signatures was quite different, and we are currently exploring it.

      Conclusion:
      Taking into account somatic copy number and mutation data, we distinguished two well-defined groups of LCNEC: an SCLC-like group, carrying alterations in MYCL1, ISR2, and in both RB1 and TP53; and a group resembling AD and SQ, with alterations in CDKN2A, TTF1, KEAP1-NFE2L2, and STK11. Although these results suggest that LCNEC might be a mix of different lung cancer subtypes, mutation clonality and expression analyses show that they are likely to be a separate entity, sharing molecular characteristics with the other lung cancer subtypes. Their heterogeneity suggests that LCNEC might represent an evolutionary trunk that can branch to SCLC or AD/SQ.

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    ORAL 41 - Immune Biology, Microenvironment and Novel Targets (ID 159)

    • Event: WCLC 2015
    • Type: Oral Session
    • Track: Biology, Pathology, and Molecular Testing
    • Presentations: 1
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      ORAL41.01 - Tumor-Infiltrating B Lymphocytes Characterized by CD79a and MUM1 Independently Predict Outcome in Patients with Non-Small Cell Lung Cancer (ID 485)

      18:30 - 20:00  |  Author(s): S. Ansén

      • Abstract
      • Presentation
      • Slides

      Background:
      Tumor-infiltrating lymphocytes play an important role in cell-mediated immune-destruction of cancer cells and tumor growth control. For non-small cell lung cancer (NSCLC) a prognostic role of T cell subtypes, natural killer cells and dendritic cells within the tumor stroma has been described. Here, we studied the role of tumor-infiltrating B cells characterized by CD79a (B-cell antigen receptor complex-associated protein alpha chain) and MUM1 surface expression (Multiple myeloma oncogene 1) in patients with NSCLC. To our knowledge, this study represents the so far largest cohort analyzing the prognostic impact of tumor-infiltrating B-cells.

      Methods:
      B cell infiltration was quantified using immunohistochemistry and antibodies to CD79a (Dako, clone JCB117) and MUM1 (Dako, clone MUM1p) on tissue microarrays (TMA) of paraffin embedded tumor sections. Genetic driver mutations were identified by next-generation sequencing and FISH analysis. SPSS version 20 (IBM Corp.) was used for statistical analysis. Chi-square test, Fisher’s exact test, Kaplan-Meier survival analysis and Cox-regression analysis were used as appropriate.

      Results:
      478 tissue samples from NSCLC patients were available for immunohistochemistry. 65% of patients were male, median age was 66 years. 56% had adenocarcinoma and 39% squamous cell histology. 61% of patients had localized disease (stage I/II), 30% locally advanced disease (stage III) and 6% were diagnosed with stage IV. Frequencies of genomic aberrations are listed in Table 1. CD79a and MUM1 positive cells were detected in 40.8% (195/478) and 40.2% (192/478) of the analyzed NSCLC tissue samples, respectively. B cell infiltration was not associated with clinical or histo-pathological characteristics. MUM1 expression was associated with a significantly prolonged overall survival (median OS 54 vs. 40 months, p=0.025). The expression of CD79a showed a trend towards a better outcome (median OS 49 vs. 40 months, p=0.069). In the multivariate analysis B cell infiltration characterized by CD79a/MUM1 positivity was an independent prognostic marker for survival (p=0.045) as was MUM1 expression (p=0.031). Table 1.

      Genomic aberration Number of patients Frequency
      TP53 mutation 136 28.5%
      KRAS mutation 65 13.6%
      FGFR1 amplification 28 5.9%
      PIK3CA mutation 17 3.6%
      EGFR mutation 12 2.5%
      ALK fusion 4 0.8%
      ERBB2 mutation 4 0.8%
      ERBB2 amplificiation 4 0.8%
      ROS1 fusion 2 0.4%
      BRAF mutation 2 0.4%
      DDR2 mutation 2 0.4%
      FGFR2 mutation 1 0.2%


      Conclusion:
      B cell infiltration characterized by immunohistochemical positivity for CD79a and MUM1 represents an independent prognostic marker in NSCLC. This finding supports the hypothesis of a B cell-mediated anti-tumor immunity.

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