Author of

• 30279

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  MA20 - Thymic Tumors: From Molecular to Clinical Results and New Challenges in Other Rare Thoracic Tumors (ID 149)

  • Event: WCLC 2019
  • Type: Mini Oral Session
  • Track: Thymoma/Other Thoracic Malignancies
  • Presentations: 1
  • Now Available
  • Moderators:Kazuya Kondo, Edith Michelle Marom
  • Coordinates: 9/10/2019, 11:30 - 13:00, San Francisco (2009)

  • 30280

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    MA20.01 - Global Quantitative Mass Spectrometry Reveals Potential Novel Actionable Targets in Thymic Epithelial Tumors (TET)   (Now Available) (ID 2294)

    11:30 - 13:00  |  Presenting Author(s): Udayan Guha
    • Abstract
    • Presentation
    • Slides

    Background
    

    Thymomas (T) and thymic carcinomas (TC), that constitute the thymic epithelial tumors (TETs) are rare epithelial tumors. There are limited treatment options for patients with advanced TETs. The complexity and rarity of the disease hampers the development of effective therapeutics. Next-generation sequencing (NGS) analyses of TETs by the TCGA have confirmed the very low mutational burden and few actionable targets for therapy. Thus, novel strategies are needed for better elucidating the molecular pathways involved in tumor pathogenesis and identification of novel drug targets. Here, we have used quantitative mass spectrometry (MS) to characterize the global proteome and phosphoproteome of TETs with aim of identifying potential actionable drivers in thymomas and thymic carcinomas.

    Method
    

    Three-state SILAC quantitative mass spectrometry was used to quantify the global proteomes and phosphoproteomes of two thymoma (IU-TAB1 and T1682) and three thymic carcinoma cell lines (MP57, T1889 and Ty82). 10-plex TMT quantitative proteomics was used to quantify the global proteomes and phosphoproteomes of 54 TET tumors. All tumor tissues were pooled together to make the reference channel and labeled with TMT¹⁰-131. Basic RPLC followed by TiO₂ enrichment and tandem MS were performed in a Q Exactive^TM HF mass spectrometer. MS data was processed using MaxQuant and Perseus. Protein quantification, normalization and statistical testing for the TMT experiments was done using free R package MSstatsTMT.

    Result
    

    We identified 4756 proteins and 5690 phosphosites from TET cell lines. Hierarchical clustering of SILAC ratios of quantitation demonstrated that T1682 and MP57 were more similar to each other than T1889 and Ty82. Several metabolic enzymes (LDHB, GSTP1, and AKR1B1) had higher expression in TC lines, while mitochondrial glutamate carrier SLC25A22 had greater abundance in thymoma lines. Ingenuity pathway analysis revealed that the top enriched canonical pathways associated with the significantly changed proteins in TET included remodeling of epithelial adherens junction, mitochondria dysfunction, and oxidative phosphorylation. RAS signaling pathway was enriched among the significantly changed phosphosites in the thymic MP57 and the B1 thymoma T1682 cells. We further analyzed the proteome and phosphoproteome of 54 TET tumor samples from 28 patients (23 thymoma and 5 thymic carcinoma) undergoing surgery or biopsy using TMT mass spectrometry. In total, 8320 proteins and 17716 phosphosites were identified. Hierarchical clustering of the TMT ratios to the pool for both proteins and phosphosites demonstrated that thymomas and thymic carcinomas clustered separately. Different locations of tumors from the same patient were grouped together. Only a few sites from the thymoma patients clustered in the thymic carcinoma group. GTF2I had higher abundance in thymomas compared to the TCs. MCM complex proteins and solute carrier family proteins had lower abundance and several collagens had higher abundance in TC patients. Several kinases, including PDGFRB, RIOK1, TNIK, and MAP4K4, and the metabolic enzyme glutathione S-transferase (GSTP1) had higher expression in TC patients. Further bioinformatics analysis and validation experiments are currently underway. Sensitivity data to inhibitors of metabolic enzymes and target kinases will be presented.

    Conclusion
    

    Global quantitative proteome and phosphoproteome analyses revealed potential novel kinases and metabolic enzymes for targeted therapy of TETs.

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• 30446

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  P1.01 - Advanced NSCLC (ID 158)

  • Event: WCLC 2019
  • Type: Poster Viewing in the Exhibit Hall
  • Track: Advanced NSCLC
  • Presentations: 1
  • Moderators:
  • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall

  • 30479

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    P1.01-27 - Serial Circulating Tumor DNA (ctDNA) Analysis of Blood and Saliva Predicts Osimertinib Response and Resistance in EGFR-Mutant NSCLC (ID 2909)

    09:45 - 18:00  |  Author(s): Udayan Guha
    • Abstract

    Background
    

    ctDNA has emerged as a promising non-invasive tool to detect lung cancer associated genomic alterations. We assessed whether serial ctDNA monitoring of plasma and saliva correlates with tumor burden and predicts response, resistance, and progression free survival to osimertinib, the 3rd generation EGFR TKI during treatment of EGFR mutated NSCLC.

    Method
    

    Plasma and saliva samples were collected at every clinic visit from patients with metastatic EGFR mutant NSCLC enrolled in a clinical trial of local ablative therapy (LAT) upon oligoprogression (5 or less sites of progression) on osimertinib (NCT02759835). Plasma ctDNA was analyzed by droplet-digital PCR (ddPCR) EGFR mutation detection and InVisionSeq Tagged-Amplicon next-generation sequencing. Saliva ctDNA was analyzed by Electric Field-Induced Release and Measurement (EFIRM) liquid biopsy (eLB) assay. Tumor burden was assessed by volumetric CT scoring of all target lesions and other soft tissue lesions ≥10 mm. ctDNA-level changes were correlated with clinical response.

    Result
    

    We analyzed 389 plasma samples from 20 patients by ddPCR, 126 plasma samples from 16 patients by NGS and 298 saliva samples from 18 patients by eLB. A high correlation between ddPCR and NGS allele frequencies (AFs) was found (Spearman g=0.96; p<0.001). Plasma ddPCR and NGS also correlated with saliva eLB assay for mutant EGFR detection (Spearman g=0.42 and 0.45, respectively; p<0.001 for both). Among 14 patients who progressed, ctDNA progression (AFs increased two consecutive times by ddPCR) predated RECIST progression by a median of 87 days (range: 28-216 days) in 8 patients. Of 6 patients without ctDNA progression, 2 patients had increase in EGFR mutation-level by eLB and 1 patient by NGS. ctDNA clearance on day 42 or 56 (2 cycles of osimertinib treatment) predicted PFS (HR=0.22, 95% CI=0.06-0.79, p=0.02; figure 1). Both baseline sensitizing EGFR mutation AF and copy number, but not baseline tumor volume, were significantly associated with PFS. Acquisition of MET, EGFR, and ERBB2 amplifications and the EGFR C797S mutation were identified as key resistance mechanisms by NGS in this cohort of patients.

    

    Conclusion
    

    Serial assessment of plasma and saliva ctDNA is clinically useful for monitoring the therapeutic response to osimertinib and for early detection of resistance mechanisms for clinical decision making. Three assays used in this study, the ddPCR and NGS for plasma ctDNA detection, and eLB for saliva ctDNA detection are complementary with each having unique advantages.