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R. Biswas



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    P1.02 - Biology/Pathology (ID 614)

    • Event: WCLC 2017
    • Type: Poster Session with Presenters Present
    • Track: Biology/Pathology
    • Presentations: 1
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      P1.02-063 - Tumor Heterogeneity Analyses by Integrated Proteo-Genomics of Thoracic Tumors from Sequential Biopsies and Warm Autopsies (ID 10355)

      09:30 - 16:00  |  Author(s): R. Biswas

      • Abstract

      Background:
      Tumor heterogeneity modulates treatment response to targeted therapy. Both intra-tumor and inter-tumor heterogeneity is well characterized in various cancers, including lung cancer, the commonest cause of cancer death in both men and women. Tumor heterogeneity studies have been conducted mostly for early stage lung cancer. Furthermore, these studies have focused primarily on next-generation sequencing (NGS).

      Method:
      We applied whole exome sequencing (WES), RNA-seq, OncoScan CNV and mass spectrometry-based proteomic analyses on 46 tumor regions from metastatic sites including lung, liver and kidney, obtained by rapid/warm autopsy from 4 patients with stage IV lung adenocarcinoma, 1 patient each with pleural mesothelioma and thymic carcinoma. 3/6 patients were admitted to NIH Clinical Center to receive in-patient hospice care before death under this study and the autopsy procedure was initiated between 2-4 hours of death in all patients. We have also performed similar integrated proteogenomics analyses on 11 different biopsies, including at autopsy of an “exceptional responder” lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for 7 years. We used the “super-SILAC” and TMT labeling strategies for quantitative proteomics using a Thermo Orbitrap Elite mass spectrometer. Patient-specific databases were built incorporating all somatic variants identified by NGS to interrogate the mass spectrometry data and an extensive validation pipeline was built for confirmation of variant peptides.

      Result:
      Here, we report an integrated analysis at the level of somatic variants, copy number, transcript, protein expression, and the phosphoproteome to demonstrate the extent of tumor heterogeneity and its potential impact on tumor biology. All tumors displayed organ-specific, branched evolution that was consistent across exome, transcriptome and proteomic analyses. RNA-seq, CNV-seq and proteomics analyses complemented the clonal evolution analyses performed using WES. The degree of heterogeneity at the genomic and proteomic level was patient-specific. There was extreme heterogeneity within the tumors of one of four patients with lung adenocarcinoma and in the thymic carcinoma patient (both non-smokers). Further examination of the heterogenous thymic and lung adenocarcinoma tumors showed strong enrichment of APOBEC-mutagenesis signature and high APOBEC3B mRNA levels. We identified a high risk APOBEC3AB germline allele in the thymic carcinoma patient that results in increased APOBEC expression and mutagenesis.

      Conclusion:
      Our integrated proteo-genomics analyses reveal significant differences in the genomic and proteomic intra-tumor and inter-tumor heterogeneity. APOBEC-mutagenesis is a significant driver of extreme cases of heterogeneity. High risk APOBEC germline alleles and increased APOBEC expression drive APOBEC mutagenesis in select patients.