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Eloisa Jantus



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    P1.03 - Biology (ID 161)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Biology
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
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      P1.03-15 - Non-Invasive Detection of Secondary Resistance Mutations in ALK-Positive NSCLC Patients by Next-Generation Sequencing (ID 1658)

      09:45 - 18:00  |  Author(s): Eloisa Jantus

      • Abstract
      • Slides

      Background

      ALK inhibitors have led to important improvements in ALK-positive non-small cell lung cancer (NSCLC) patient’s survival and quality of life. However, despite the good responses, resistance mutations inevitably emerge. Several resistance mutations in ALK domain have been describe. Remarkably different mutations can confer different sensitivities to different ALK inhibitors. However, 2nd and 3rd line treatment is often prescribe empirically without knowing the molecular mechanism underlying treatment failure.

      Method

      21 samples from ALK-positive NSCLC patients were collected at disease progression. Circulating Nucleic Acids were isolated from platelets, exosomes and plasma. Libraries were prepared using 20ng of template and Oncomine™ Pan-Cancer Cell-Free Assay. Samples were sequenced on an Ion GeneStudio S5 Plus System. Sequencing data was first analyzed using Torrent Suite software. Subsequently variant calling, annotation and filtering was performed on the Ion Reporter (v5.10) platform using the Oncomine TagSeq Pan-Cancer Liquid Biopsy w2.1 workflow.

      Result

      In 14 (67%) patients a somatic mutation was identified in the plasma sample collected at disease progression. The average number of mutations detected per sample was 2.6. Noteworthy, 14 mutations were found in oncogenes that have been previously associated with ALK inhibitors resistance (5 mutations in ALK locus, 4 mutations in PIK3CA, 1 mutation in EGFR, 1 mutation in KIT, 1 mutation in KRAS, 1 mutation in MTOR and 1 mutation in MYC). The rest of mutations (N=21) were found in TP53 gene. Secondary resistance mutation in ALK locus occurred in 24% of the cases. Specifically, p.G1269A (N=2), p.G1202E (N=1), p.R1275Q (N=1) mutations were found in ALK-positive NSCLC who had progressed on crizotinib and p.G1202R mutation was found in 1 ALK-positive NSCLC who had progressed on ceritinib.

      Conclusion

      Secondary ALK-TKI resistance mutations could be detected using liquid biopsies in a high proportion of patients. Non-invasive molecular profiling of samples collected at disease progression is feasible being useful for further treatment selection in ALK-positive NSCLC patients.

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    P1.09 - Pathology (ID 173)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Pathology
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
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      P1.09-13 - Prognostic Value of TMPRSS4 Expression and Its Role as Diagnostic Biomarker by Liquid Biopsy in Early Stage NSCLC (ID 2499)

      09:45 - 18:00  |  Author(s): Eloisa Jantus

      • Abstract
      • Slides

      Background

      Relapse rates in surgically-resected non-small cell lung cancer (NSCLC) patients are between 30-45% within 5 years of diagnosis, which reflects the clinical need to identify those patients at high risk of recurrence and death. TMPRSS4 is a serine protease that plays a role in lung cancer growth, development of metastasis and resistance to chemotherapy in NSCLC models. TMPRSS4 is overexpressed through promoter hypomethylation in NSCLC tumors.

      Method

      Two cohorts of NSCLC patients (MD Anderson (MDA), n=489; and Clinica Universidad de Navarra (CUN), n=95) were used to investigate the prognostic value of TMPRSS4. The WHO 2004 classification and 8th TNM edition was used for tumor stratification. We have also developed a method to quantify he degree of TMPRSS4 and SHOX2 methylation status in liquid biopsy (plasma and bronchoalveolar lavages (BALS)) by digital droplet PCR (ddPCR), in tumor-free individuals and patients with NSCLC.

      Result

      High levels of TMPRSS4 were significantly associated with reduced relapse-free survival (RFS, p<0.001) and overall survival (OS, p<0.001) in the MDA cohort, and with OS in the CUN cohort (p<0.049). In univariate Cox regression analysis using the MDA cohort, high TMPRSS4 levels were RFS (HR=2.09; 95% IC [1.53-2.87], p<0.001) and OS (HR=1.82; 95% IC [1.38-2.41], p<0.001). In multivariate analyses, TMPRSS4 was found as an independent prognostic factor for both RFS (HR=1.82, IC [1.28-2.60], p<0.001) and OS (HR=1.44, IC [1.07-1.94], p<0.014).
      In our MDA cohort, stage IA and stage IB showed no statistical differences for RFS (p=0.27) or OS (p<0.001). However, when considering the protein expression of TMPRSS4 we were able to substratify stage IA patients in low and high risk patients, since those with high TMPRSS4 levels showed a significantly reduced RFS (p=0.002) and OS (p<0.001). Similar tendency was observed for stage IB, although statistical differences were not found.

      After successful establishment of the ddPCR conditions for TMPRSS4 and SHOX2 methylation status, we analyzed plasmas and BALS in case-control studies. In BALS (79 NSCLC patients and 26 controls), significant hypomethylation (p<0.01) was found for TMPRSS4 in the case of patients with early stage NSCLC in comparison with controls, with an AUROC of 0.72 (95% IC, 0.57-0.87) (p=0.008). SHOX2 was significantly hypermethylated in BALS from early stage NSCLC compared to controls (p<0.01), with an AUROC of 0.71 (95% IC, 0.56- 0.86) (p=0.01). In the case of plasmas (89 NSCLC patients and 25 controls): in early stages, a significant hypomethylation was found for TMPRSS4 (p<0.05), with an AUROC of 0.73 (95% IC, 0.54-0.90) (p=0.015). For SHOX2, only late stages NSCLC showed significant hypermethylation with respect to controls (p<0.05), with an AUROC of 0.68 (95% IC, 0.54-0.80) (p=0.025).

      Conclusion

      High TMPRSS4 levels are associated with worse prognosis in NSCLC patients. TMPRSS4 expression significantly discriminates patients with higher risk of disease progression and poor survival outcome in early stage NSCLC. Methylation status of TMPRSS4 can be used in both plasma and BALS to identify patients with NSCLC.

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    P2.03 - Biology (ID 162)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Biology
    • Presentations: 3
    • Moderators:
    • Coordinates: 9/09/2019, 10:15 - 18:15, Exhibit Hall
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      P2.03-16 - Agreement Between Different Methodologies for Non-Invasive p.T790M and EGFR Sensitizing Mutation Testing (ID 1965)

      10:15 - 18:15  |  Author(s): Eloisa Jantus

      • Abstract
      • Slides

      Background

      Tyrosine kinase inhibitors (TKIs) are the current standard of care for patients with advanced EGFR-mutant non-small cell lung cancer (NSCLC). However, most patients progressed within 1 to 2 years. The EGFR p.T790M mutation is the most common resistance mechanism to first and second generation EGFR TKIs. The identification of p.T790M mutation is of considerable clinical relevance as osimertinib has demonstrated clinical efficacy in this setting. Guidelines recommend testing for the p.T790M mutation in blood at relapse to TKIs, and re-biopsy only in case of a negative result. Several blood based methodologies for detection of EGFR mutations have been developed in the recent years. However, the number of comparison studies between platforms is very limited.

      Method

      This is a multicenter, cross-sectional study (ClinicalTrials.gov Identifier: NCT03363139) performed by the Spanish Lung Cancer Group. Samples from 75 consecutive EGFR mutant NSCLC patients were collected at disease progression to first line TKI treatment. The presence of EGFR mutations in the cfDNA was evaluated in 39 samples by 7 methodologies, namely: Cobas® EGFR Mutation Test v2 (Roche Diagnostics), Therascreen EGFR Plasma RGQ PCR Kit (Qiagen), QuantStudio® 3D Digital PCR System (Thermofisher), a 5′-nuclease real-time PCR (TaqMan®) assay in presence of PNA, OncoBEAM EGFR (Sysmex Inostics), NGS with two different gene panels: Oncomine® (Thermofisher) and Lung Cancer Panel (Qiagen). The agreement between methodologies was assessed using the kappa coefficient (K) and its corresponding 95% confidence intervals (95% CI). For quantitative variables the concordance correlation coefficient (ccc) was used.

      Result

      Complete results are available for 39 patients. Overall, the agreement between all methodologies for the detection of p.T790M mutation as well as the original EGFR sensitizing mutation was good (K=0.669; 95CI: 0.504-0.835 and K=0.750 95CI: 0.599-0.899 respectively). Remarkably, the agreement between FDA-approved methodologies for p.T790M detection was almost perfect (K=0.926; 95CI: 0.712-1) and good for the EGFR sensitizing mutations (K=0.657; 95CI: 0.417-0.902). Similarly, the agreement between NGS-based methodologies for the detection of p.T790M and the EGFR activating mutations was very high (K=0.843; 95CI: 0.567-1 and K=0.872 95CI: 0.595-1 respectively). Moreover, concordance between both technologies for p.T790M and EGFR sensitizing mutation mutant allele frequency was excellent (ccc=0.956; 95CI: 0.906-1 and ccc=0.980 95CI: 0.950-1 respectively). The proportion of samples that were positive for p.T790M detection varied from 28% (PCR based technologies) to 37% depending on the methodology.

      Conclusion

      NGS and PCR-based methodologies show a good to excellent agreement for the detection of EGFR mutations, including the p.T790M. Our results support the use of liquid biopsies for non-invasive testing of clinically relevant mutations (Data from the whole cohort will be presented at the meeting).

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      P2.03-33 - ctDNA Levels Significantly Predicts Survival in NSCLC Patients with an EGFR Activating Mutation (ID 2016)

      10:15 - 18:15  |  Author(s): Eloisa Jantus

      • Abstract

      Background

      Circulating tumor DNA (ctDNA) have been shown to be useful for non-invasive biomarker testing in non-small cell lung cancer (NSCLC). In addition, there is growing evidence supporting that ctDNA levels can be useful for tumor response to treatment monitoring. Nevertheless, data from large prospective clinical longitudinal studies still limited.

      Method

      300 plasma samples from 100 advanced NSCLC patients, with tumors harboring an EGFR activating mutation and treated with a first line tyrosine Kinase inhibitor were analyzed. Samples were collected before the start of treatment, at first follow up evaluation, at 7 month and at disease progression. ctDNA was analyzed by dPCR.

      Result

      Median follow up was 11.3 months. There were not significant differences in progression free survival (PFS) or overall survival (OS) according to treatment (erlotinib, afatinib or gefitinib). Patients harboring a deletion in exon 19 or a mutation in exon 21 exhibited better survival than those with an insertion in exon 20 (P<0.001). dPCR detected EGFR sensitizing mutation in 77% of the pre-treatment samples. ctDNA levels before the start of the treatment did not significantly predict survival, although a tendency was observed, with patients with high levels of ctDNA showing poorer outcome. On the contrary, patients in which the EGFR sensitizing mutation was undetectable at first follow up had a markedly better PFS and OS (HR=2.7; 95IC= 1.4-5.5 and HR= 5.5 95IC: 1.8-17 respectively). In the same way, patients in which the EGFR sensitizing mutation remained negative at 7months had a significantly increased PFS (HR: 2.8; 95IC: 1.2-6.6). None of the patients with undetectable levels at 7 months has deceased.

      Conclusion

      ctDNA levels is of prognostic significance in EGFR positive NSCLC patients with advance disease and can be useful to monitor treatment outcome

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      P2.03-38 - Identification of a Novel Synthetic Lethal Vulnerability in Non-Small Cell Lung Cancer by Co-Targeting TMPRSS4 and DDR1 (ID 2191)

      10:15 - 18:15  |  Author(s): Eloisa Jantus

      • Abstract
      • Slides

      Background

      Synthetic lethality has been defined as the inability of cells to proliferate when co-targeting two genes, with a synergistically superior inhibition than that found for each individual gene. Consistent co-expression of two genes involved in a similar function is a predictor of synthetic lethality, a strategy that is being applied to find out novel cancer vulnerabilities.

      Method

      Large-scale bioinformatics analyses across 5 public databases were used to identify genes consistently co-expressed with TMPRSS4, a novel therapeutic target that we have previously identified in NSCLC. Pyrosequencing was used to evaluate methylation levels in patients and cell lines. Functional in vitro experiments and animal models were used to assess synthetic lethality of TMPRSS4 and DDR1 in NSCLC.

      Result

      Consistent co-expression between TMPRSS4 and DDR1 was found in all NSCLC databases evaluated. Similar to TMPRSS4, DDR1 promoter was hypomethylated in NSCLC in 3 independent cohorts and hypomethylation was an independent prognostic factor of disease-free survival. Treatment with 5-azacitidine increased DDR1 levels in cell lines, suggesting an epigenetic regulation. Cells lacking TMPRSS4 were highly sensitive to the cytotoxic effect of the DDR1 inhibitor dasatinib. TMPRSS4/DDR1 double knock-down cells, but not single knock-out cells suffered a G0/G1 cell cycle arrest with loss of E2F1 and cyclins A and B, increased p21 levels and apoptosis. Moreover, double knock-down cells were highly sensitized to cisplatin, which caused massive apoptosis (~40%). In vivo studies demonstrated tumor regression in mice injected with double knock-down-injected cells and lack of 18FDG-uptake by microPET analysis.

      Conclusion

      We have identified a novel vulnerability in NSCLC resulting from a synthetic lethal interaction between DDR1 and TMPRSS4. This may help designing therapeutic strategies to impair NSCLC growth by co-targeting both genes.

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    P2.05 - Interventional Diagnostic/Pulmonology (ID 168)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Interventional Diagnostics/Pulmonology
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/09/2019, 10:15 - 18:15, Exhibit Hall
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      P2.05-10 - Liquid Biopsy: Association Between the Burden of Disease in Patients with EGFR-Mutated NSCLC and the Frequency of Its Detection in Blood (ID 2384)

      10:15 - 18:15  |  Author(s): Eloisa Jantus

      • Abstract
      • Slides

      Background

      In the management of patient’s whit non small cell lung cancer (NSCLC) with EGFR mutations after progression to first and second generation tyrosine kinasa inhibitors (TKI), the mechanism of resistance is very important. Our objective is to analyse the appearance kinetics of the T790M by means of digital PCR techniques in liquid biopsy.

      Method

      We conducted a multicenter study with 100 patients with EGFR-mutated NSCLC, treated with first-line TKI therapy. We analyze the ctDNA by dPCR before the start of treatment, at first follow up evaluation, at 6 months and at disease progression.

      Result

      We included a total of 100 patients from July 2016 to December of 2017. Seven patients with Exon 20 insertion in EGFR were excluded (final sample 93). The median of follow-up was 12 months. There were not significant differences in progression free survival (PFS) or overall survival (OS) according to treatment (erlotinib, gefitinib or afatinib). dPCR detected EGFR sensitizing mutation in 77% of the pre-treatment samples. Of these cases, EGFR sensitizing mutation was detected in 75% of the patients with stage IVA and 85% in stage IVB respectively, p=0,075. The resistance mutation p.T790M was detected in 52% of the samples collected at disease progression. The probability to detect the resistance mutation p.T790M by liquid biopsy, is greater if the pre-treatment sample was positive for EGFR sensitizing mutation (11% vs 62%) p 0,009. In cases with progression of the disease the percent of detection of p.T790M was 52% and 54% in patients with Exon 19 deletion and L858R mutation respectively. The OS in patients with progression of the disease and p.T790M negative was 85% at 12 months (95%CI: 60%-94%) and 75% with p.T790M positive (95%CI: 49%-88%), p=0,01.

      Conclusion

      The burden of disease in patients with NSCLC mutated with EGFR is related to the appearance of sensitivity and resistance mutations in liquid biopsy. The probability to detect the resistance mutation p.T790M in blood, is greater if the pre-treatment sample was positive for EGFR sensitizing mutation.

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